NP-MRD: Showing NP-Card for Pyloricidin D (NP0004004)

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Record Information

Version

1.0

Created at

2020-12-09 01:31:38 UTC

Updated at

2021-07-15 16:47:58 UTC

NP-MRD ID

NP0004004

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pyloricidin D

Provided By

NPAtlas

Description

Pyloricidin D is found in Bacillus. It was first documented in 2001 (PMID: 11827035). Based on a literature review very few articles have been published on (3R)-3-{[(2R,3S,4S,5R)-5-amino-1,2,3,4,6-pentahydroxyhexylidene]amino}-3-phenylpropanoic acid.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242118033D          

 46 46  0  0  0  0            999 V2000
    3.9069   -1.6839    0.9585 N   0  0  2  0  0  0  0  0  0  0  0  0
    4.1041   -0.3958    0.2910 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.6212   -0.2447    0.1455 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.2518   -0.2576    1.3831 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5923    0.7132    1.1745 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.3513    0.6530    2.3660 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1238    0.5824    1.5043 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8456   -0.6228    2.1216 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2748    0.8711    0.3033 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4210   -0.1123   -0.6426 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1601    0.9914    0.6577 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4721    1.8559    1.5146 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1068    0.1523    0.0373 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4968    0.2746    0.3867 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9915   -0.9287    1.0929 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9122   -2.2050    0.4026 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4590   -2.4623   -0.7218 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4218   -3.3158    1.1060 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3783    0.7141   -0.6971 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4404    1.5703   -0.3795 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2983    2.0300   -1.3527 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1659    1.6806   -2.6795 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1273    0.8397   -3.0109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2516    0.3696   -2.0236 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5909   -1.8031    1.7301 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0035   -2.4736    0.2776 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6847   -0.3722   -0.7272 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8491    0.6837   -0.4328 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0156   -1.0877   -0.4693 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5474   -1.1996    1.5706 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8083    1.6910    0.7057 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9501   -0.0146    2.9896 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9184    1.4021    2.2787 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0399   -1.0723    1.8085 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6377    1.8680   -0.1036 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1825   -0.9753   -0.2241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7603   -0.5439   -0.6694 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5299    1.1132    1.1671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0486   -0.7548    1.4244 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3805   -1.0322    2.0362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3803   -3.3382    1.4259 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5743    1.8685    0.6706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1300    2.6975   -1.1194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8235    2.0253   -3.4645 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9766    0.5295   -4.0569 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4346   -0.2807   -2.2904 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
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 13 14  1  0  0  0  0
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 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
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 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
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  1 25  1  0  0  0  0
  1 26  1  0  0  0  0
  2 27  1  6  0  0  0
  3 28  1  0  0  0  0
  3 29  1  0  0  0  0
  4 30  1  0  0  0  0
  5 31  1  6  0  0  0
  6 32  1  0  0  0  0
  7 33  1  1  0  0  0
  8 34  1  0  0  0  0
  9 35  1  6  0  0  0
 10 36  1  0  0  0  0
 13 37  1  0  0  0  0
 14 38  1  1  0  0  0
 15 39  1  0  0  0  0
 15 40  1  0  0  0  0
 18 41  1  0  0  0  0
 20 42  1  0  0  0  0
 21 43  1  0  0  0  0
 22 44  1  0  0  0  0
 23 45  1  0  0  0  0
 24 46  1  0  0  0  0
M  END

     RDKit          3D

 46 46  0  0  0  0  0  0  0  0999 V2000
    3.9069   -1.6839    0.9585 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1041   -0.3958    0.2910 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.6212   -0.2447    0.1455 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2518   -0.2576    1.3831 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5923    0.7132    1.1745 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.3513    0.6530    2.3660 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1238    0.5824    1.5043 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8456   -0.6228    2.1216 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2748    0.8711    0.3033 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4210   -0.1123   -0.6426 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1601    0.9914    0.6577 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4721    1.8559    1.5146 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1068    0.1523    0.0373 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4968    0.2746    0.3867 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9915   -0.9287    1.0929 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9122   -2.2050    0.4026 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4590   -2.4623   -0.7218 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4218   -3.3158    1.1060 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3783    0.7141   -0.6971 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4404    1.5703   -0.3795 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2983    2.0300   -1.3527 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1659    1.6806   -2.6795 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1273    0.8397   -3.0109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2516    0.3696   -2.0236 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5909   -1.8031    1.7301 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0035   -2.4736    0.2776 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6847   -0.3722   -0.7272 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8491    0.6837   -0.4328 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0156   -1.0877   -0.4693 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5474   -1.1996    1.5706 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8083    1.6910    0.7057 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9501   -0.0146    2.9896 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9184    1.4021    2.2787 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0399   -1.0723    1.8085 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6377    1.8680   -0.1036 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1825   -0.9753   -0.2241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7603   -0.5439   -0.6694 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5299    1.1132    1.1671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0486   -0.7548    1.4244 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3805   -1.0322    2.0362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3803   -3.3382    1.4259 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5743    1.8685    0.6706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1300    2.6975   -1.1194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8235    2.0253   -3.4645 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9766    0.5295   -4.0569 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4346   -0.2807   -2.2904 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  2  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
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  9 10  1  0
  9 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
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 16 17  2  0
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 22 23  1  0
 23 24  2  0
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  5 31  1  6
  6 32  1  0
  7 33  1  1
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M  END


  Mrv1652306242118033D          

 46 46  0  0  0  0            999 V2000
    3.9069   -1.6839    0.9585 N   0  0  2  0  0  0  0  0  0  0  0  0
    4.1041   -0.3958    0.2910 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.6212   -0.2447    0.1455 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.2518   -0.2576    1.3831 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5923    0.7132    1.1745 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.3513    0.6530    2.3660 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1238    0.5824    1.5043 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8456   -0.6228    2.1216 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2748    0.8711    0.3033 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4210   -0.1123   -0.6426 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1601    0.9914    0.6577 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.1068    0.1523    0.0373 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4968    0.2746    0.3867 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9915   -0.9287    1.0929 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9122   -2.2050    0.4026 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4590   -2.4623   -0.7218 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4218   -3.3158    1.1060 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3783    0.7141   -0.6971 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4404    1.5703   -0.3795 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2983    2.0300   -1.3527 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1659    1.6806   -2.6795 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1273    0.8397   -3.0109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2516    0.3696   -2.0236 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5909   -1.8031    1.7301 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0035   -2.4736    0.2776 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6847   -0.3722   -0.7272 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8491    0.6837   -0.4328 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0156   -1.0877   -0.4693 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5474   -1.1996    1.5706 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8083    1.6910    0.7057 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9501   -0.0146    2.9896 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9184    1.4021    2.2787 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0399   -1.0723    1.8085 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6377    1.8680   -0.1036 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.3805   -1.0322    2.0362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3803   -3.3382    1.4259 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5743    1.8685    0.6706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1300    2.6975   -1.1194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8235    2.0253   -3.4645 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9766    0.5295   -4.0569 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4346   -0.2807   -2.2904 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
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 14 15  1  0  0  0  0
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 16 18  1  0  0  0  0
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  2 27  1  6  0  0  0
  3 28  1  0  0  0  0
  3 29  1  0  0  0  0
  4 30  1  0  0  0  0
  5 31  1  6  0  0  0
  6 32  1  0  0  0  0
  7 33  1  1  0  0  0
  8 34  1  0  0  0  0
  9 35  1  6  0  0  0
 10 36  1  0  0  0  0
 13 37  1  0  0  0  0
 14 38  1  1  0  0  0
 15 39  1  0  0  0  0
 15 40  1  0  0  0  0
 18 41  1  0  0  0  0
 20 42  1  0  0  0  0
 21 43  1  0  0  0  0
 22 44  1  0  0  0  0
 23 45  1  0  0  0  0
 24 46  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0004004

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)C([H])([H])[C@@]([H])(N([H])C(=O)[C@]([H])(O[H])[C@@]([H])(O[H])[C@@]([H])(O[H])[C@]([H])(N([H])[H])C([H])([H])O[H])C1=C([H])C([H])=C([H])C([H])=C1[H]

> <INCHI_IDENTIFIER>
InChI=1S/C15H22N2O7/c16-9(7-18)12(21)13(22)14(23)15(24)17-10(6-11(19)20)8-4-2-1-3-5-8/h1-5,9-10,12-14,18,21-23H,6-7,16H2,(H,17,24)(H,19,20)/t9-,10-,12+,13+,14-/m1/s1

> <INCHI_KEY>
GVOBXKQKXYPNTR-SJVBDLOYSA-N

> <FORMULA>
C15H22N2O7

> <MOLECULAR_WEIGHT>
342.348

> <EXACT_MASS>
342.142701056

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
46

> <JCHEM_AVERAGE_POLARIZABILITY>
33.51226713557239

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R)-3-[(2R,3S,4S,5R)-5-amino-2,3,4,6-tetrahydroxyhexanamido]-3-phenylpropanoic acid

> <ALOGPS_LOGP>
-2.43

> <JCHEM_LOGP>
-4.865078237465461

> <ALOGPS_LOGS>
-1.55

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.010319112402563

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.7694052380894085

> <JCHEM_PKA_STRONGEST_BASIC>
8.30471877780467

> <JCHEM_POLAR_SURFACE_AREA>
173.34

> <JCHEM_REFRACTIVITY>
81.71420000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.66e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R)-3-[(2R,3S,4S,5R)-5-amino-2,3,4,6-tetrahydroxyhexanamido]-3-phenylpropanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 46 46  0  0  0  0  0  0  0  0999 V2000
    3.9069   -1.6839    0.9585 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1041   -0.3958    0.2910 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.6212   -0.2447    0.1455 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2518   -0.2576    1.3831 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5923    0.7132    1.1745 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.3513    0.6530    2.3660 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1238    0.5824    1.5043 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8456   -0.6228    2.1216 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2748    0.8711    0.3033 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4210   -0.1123   -0.6426 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1601    0.9914    0.6577 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4721    1.8559    1.5146 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1068    0.1523    0.0373 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4968    0.2746    0.3867 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9915   -0.9287    1.0929 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9122   -2.2050    0.4026 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4590   -2.4623   -0.7218 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4218   -3.3158    1.1060 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3783    0.7141   -0.6971 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4404    1.5703   -0.3795 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2983    2.0300   -1.3527 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1659    1.6806   -2.6795 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1273    0.8397   -3.0109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2516    0.3696   -2.0236 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5909   -1.8031    1.7301 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0035   -2.4736    0.2776 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6847   -0.3722   -0.7272 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8491    0.6837   -0.4328 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0156   -1.0877   -0.4693 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5474   -1.1996    1.5706 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8083    1.6910    0.7057 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9501   -0.0146    2.9896 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9184    1.4021    2.2787 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0399   -1.0723    1.8085 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6377    1.8680   -0.1036 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1825   -0.9753   -0.2241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7603   -0.5439   -0.6694 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5299    1.1132    1.1671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0486   -0.7548    1.4244 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3805   -1.0322    2.0362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3803   -3.3382    1.4259 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5743    1.8685    0.6706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1300    2.6975   -1.1194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8235    2.0253   -3.4645 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9766    0.5295   -4.0569 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4346   -0.2807   -2.2904 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  2  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 14 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 23 24  2  0
 24 19  1  0
  1 25  1  0
  1 26  1  0
  2 27  1  6
  3 28  1  0
  3 29  1  0
  4 30  1  0
  5 31  1  6
  6 32  1  0
  7 33  1  1
  8 34  1  0
  9 35  1  6
 10 36  1  0
 13 37  1  0
 14 38  1  1
 15 39  1  0
 15 40  1  0
 18 41  1  0
 20 42  1  0
 21 43  1  0
 22 44  1  0
 23 45  1  0
 24 46  1  0
M  END

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  N   UNK     0       3.907  -1.684   0.959  0.00  0.00           N+0
HETATM    2  C   UNK     0       4.104  -0.396   0.291  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.621  -0.245   0.146  0.00  0.00           C+0
HETATM    4  O   UNK     0       6.252  -0.258   1.383  0.00  0.00           O+0
HETATM    5  C   UNK     0       3.592   0.713   1.175  0.00  0.00           C+0
HETATM    6  O   UNK     0       4.351   0.653   2.366  0.00  0.00           O+0
HETATM    7  C   UNK     0       2.124   0.582   1.504  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.846  -0.623   2.122  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.275   0.871   0.303  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.421  -0.112  -0.643  0.00  0.00           O+0
HETATM   11  C   UNK     0      -0.160   0.991   0.658  0.00  0.00           C+0
HETATM   12  O   UNK     0      -0.472   1.856   1.515  0.00  0.00           O+0
HETATM   13  N   UNK     0      -1.107   0.152   0.037  0.00  0.00           N+0
HETATM   14  C   UNK     0      -2.497   0.275   0.387  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.991  -0.929   1.093  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.912  -2.205   0.403  0.00  0.00           C+0
HETATM   17  O   UNK     0      -2.459  -2.462  -0.722  0.00  0.00           O+0
HETATM   18  O   UNK     0      -3.422  -3.316   1.106  0.00  0.00           O+0
HETATM   19  C   UNK     0      -3.378   0.714  -0.697  0.00  0.00           C+0
HETATM   20  C   UNK     0      -4.440   1.570  -0.380  0.00  0.00           C+0
HETATM   21  C   UNK     0      -5.298   2.030  -1.353  0.00  0.00           C+0
HETATM   22  C   UNK     0      -5.166   1.681  -2.680  0.00  0.00           C+0
HETATM   23  C   UNK     0      -4.127   0.840  -3.011  0.00  0.00           C+0
HETATM   24  C   UNK     0      -3.252   0.370  -2.024  0.00  0.00           C+0
HETATM   25  H   UNK     0       4.591  -1.803   1.730  0.00  0.00           H+0
HETATM   26  H   UNK     0       4.003  -2.474   0.278  0.00  0.00           H+0
HETATM   27  H   UNK     0       3.685  -0.372  -0.727  0.00  0.00           H+0
HETATM   28  H   UNK     0       5.849   0.684  -0.433  0.00  0.00           H+0
HETATM   29  H   UNK     0       6.016  -1.088  -0.469  0.00  0.00           H+0
HETATM   30  H   UNK     0       6.547  -1.200   1.571  0.00  0.00           H+0
HETATM   31  H   UNK     0       3.808   1.691   0.706  0.00  0.00           H+0
HETATM   32  H   UNK     0       3.950  -0.015   2.990  0.00  0.00           H+0
HETATM   33  H   UNK     0       1.918   1.402   2.279  0.00  0.00           H+0
HETATM   34  H   UNK     0       1.040  -1.072   1.809  0.00  0.00           H+0
HETATM   35  H   UNK     0       1.638   1.868  -0.104  0.00  0.00           H+0
HETATM   36  H   UNK     0       1.183  -0.975  -0.224  0.00  0.00           H+0
HETATM   37  H   UNK     0      -0.760  -0.544  -0.669  0.00  0.00           H+0
HETATM   38  H   UNK     0      -2.530   1.113   1.167  0.00  0.00           H+0
HETATM   39  H   UNK     0      -4.049  -0.755   1.424  0.00  0.00           H+0
HETATM   40  H   UNK     0      -2.381  -1.032   2.036  0.00  0.00           H+0
HETATM   41  H   UNK     0      -4.380  -3.338   1.426  0.00  0.00           H+0
HETATM   42  H   UNK     0      -4.574   1.869   0.671  0.00  0.00           H+0
HETATM   43  H   UNK     0      -6.130   2.697  -1.119  0.00  0.00           H+0
HETATM   44  H   UNK     0      -5.824   2.025  -3.465  0.00  0.00           H+0
HETATM   45  H   UNK     0      -3.977   0.530  -4.057  0.00  0.00           H+0
HETATM   46  H   UNK     0      -2.435  -0.281  -2.290  0.00  0.00           H+0
CONECT    1    2   25   26                                                  
CONECT    2    1    3    5   27                                             
CONECT    3    2    4   28   29                                             
CONECT    4    3   30                                                       
CONECT    5    2    6    7   31                                             
CONECT    6    5   32                                                       
CONECT    7    5    8    9   33                                             
CONECT    8    7   34                                                       
CONECT    9    7   10   11   35                                             
CONECT   10    9   36                                                       
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   37                                                  
CONECT   14   13   15   19   38                                             
CONECT   15   14   16   39   40                                             
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   41                                                       
CONECT   19   14   20   24                                                  
CONECT   20   19   21   42                                                  
CONECT   21   20   22   43                                                  
CONECT   22   21   23   44                                                  
CONECT   23   22   24   45                                                  
CONECT   24   23   19   46                                                  
CONECT   25    1                                                            
CONECT   26    1                                                            
CONECT   27    2                                                            
CONECT   28    3                                                            
CONECT   29    3                                                            
CONECT   30    4                                                            
CONECT   31    5                                                            
CONECT   32    6                                                            
CONECT   33    7                                                            
CONECT   34    8                                                            
CONECT   35    9                                                            
CONECT   36   10                                                            
CONECT   37   13                                                            
CONECT   38   14                                                            
CONECT   39   15                                                            
CONECT   40   15                                                            
CONECT   41   18                                                            
CONECT   42   20                                                            
CONECT   43   21                                                            
CONECT   44   22                                                            
CONECT   45   23                                                            
CONECT   46   24                                                            
MASTER        0    0    0    0    0    0    0    0   46    0   92    0
END

RDKit          3D

46 46  0  0  0  0  0  0  0  0999 V2000
    3.9069   -1.6839    0.9585 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1041   -0.3958    0.2910 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.6212   -0.2447    0.1455 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2518   -0.2576    1.3831 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5923    0.7132    1.1745 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.3513    0.6530    2.3660 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1238    0.5824    1.5043 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8456   -0.6228    2.1216 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2748    0.8711    0.3033 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4210   -0.1123   -0.6426 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1601    0.9914    0.6577 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4721    1.8559    1.5146 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1068    0.1523    0.0373 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4968    0.2746    0.3867 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9915   -0.9287    1.0929 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9122   -2.2050    0.4026 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4590   -2.4623   -0.7218 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4218   -3.3158    1.1060 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3783    0.7141   -0.6971 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4404    1.5703   -0.3795 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2983    2.0300   -1.3527 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1659    1.6806   -2.6795 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1273    0.8397   -3.0109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2516    0.3696   -2.0236 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5909   -1.8031    1.7301 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0035   -2.4736    0.2776 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6847   -0.3722   -0.7272 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8491    0.6837   -0.4328 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0156   -1.0877   -0.4693 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5474   -1.1996    1.5706 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8083    1.6910    0.7057 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9501   -0.0146    2.9896 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9184    1.4021    2.2787 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0399   -1.0723    1.8085 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6377    1.8680   -0.1036 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1825   -0.9753   -0.2241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7603   -0.5439   -0.6694 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5299    1.1132    1.1671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0486   -0.7548    1.4244 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3805   -1.0322    2.0362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3803   -3.3382    1.4259 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5743    1.8685    0.6706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1300    2.6975   -1.1194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8235    2.0253   -3.4645 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9766    0.5295   -4.0569 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4346   -0.2807   -2.2904 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  2  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 14 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 23 24  2  0
 24 19  1  0
  1 25  1  0
  1 26  1  0
  2 27  1  6
  3 28  1  0
  3 29  1  0
  4 30  1  0
  5 31  1  6
  6 32  1  0
  7 33  1  1
  8 34  1  0
  9 35  1  6
 10 36  1  0
 13 37  1  0
 14 38  1  1
 15 39  1  0
 15 40  1  0
 18 41  1  0
 20 42  1  0
 21 43  1  0
 22 44  1  0
 23 45  1  0
 24 46  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
(3R)-3-{[(2R,3S,4S,5R)-5-amino-1,2,3,4,6-pentahydroxyhexylidene]amino}-3-phenylpropanoate	Generator

Chemical Formula

C₁₅H₂₂N₂O₇

Average Mass

342.3480 Da

Monoisotopic Mass

342.14270 Da

IUPAC Name

(3R)-3-[(2R,3S,4S,5R)-5-amino-2,3,4,6-tetrahydroxyhexanamido]-3-phenylpropanoic acid

Traditional Name

(3R)-3-[(2R,3S,4S,5R)-5-amino-2,3,4,6-tetrahydroxyhexanamido]-3-phenylpropanoic acid

CAS Registry Number

Not Available

SMILES

N[C@H](CO)[C@H](O)[C@H](O)[C@@H](O)C(=O)N[C@H](CC(O)=O)C1=CC=CC=C1

InChI Identifier

InChI=1S/C15H22N2O7/c16-9(7-18)12(21)13(22)14(23)15(24)17-10(6-11(19)20)8-4-2-1-3-5-8/h1-5,9-10,12-14,18,21-23H,6-7,16H2,(H,17,24)(H,19,20)/t9-,10-,12+,13+,14-/m1/s1

InChI Key

GVOBXKQKXYPNTR-SJVBDLOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Bacillus	NPAtlas	11827035

Species Where Detected

Species Name	Source	Reference
Bacillus sp. HC-72	KNApSAcK Database	22123792

Chemical Taxonomy

Classification

Not classified

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-2.4	ALOGPS
logP	-4.9	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	3.77	ChemAxon
pKa (Strongest Basic)	8.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	173.34 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	81.71 m³·mol⁻¹	ChemAxon
Polarizability	33.51 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA001131

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

78436368

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139583404

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Nakao M, Miyagaw K, Nakano Y, Sakane T, Tada M, Nishimura O, Fujino M: Pyloricidins, novel anti-helicobacterpylori antibiotics produced by Bacillus sp. I. Taxonomy, fermentation and biological activity. J Antibiot (Tokyo). 2001 Nov;54(11):926-33. doi: 10.7164/antibiotics.54.926. [PubMed:11827035 ]

Showing NP-Card for Pyloricidin D (NP0004004)

MOL for NP0004004 (Pyloricidin D)

3D MOL for NP0004004 (Pyloricidin D)

3D SDF for NP0004004 (Pyloricidin D)

3D-SDF for NP0004004 (Pyloricidin D)

PDB for NP0004004 (Pyloricidin D)

3D PDB for NP0004004 (Pyloricidin D)

SMILES for NP0004004 (Pyloricidin D)

INCHI for NP0004004 (Pyloricidin D)

Structure for NP0004004 (Pyloricidin D)

3D Structure for NP0004004 (Pyloricidin D)