NP-MRD: Showing NP-Card for Negamycin (NP0021548)

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Record Information

Version

1.0

Created at

2021-01-06 06:50:28 UTC

Updated at

2021-07-15 17:36:38 UTC

NP-MRD ID

NP0021548

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Negamycin

Provided By

NPAtlas

Description

Negamycin is found in Streptomyces and Streptomyces No. M890-C2. It was first documented in 1971 (PMID: 5121145). Based on a literature review very few articles have been published on 2-({[(3R,5R)-3,6-diamino-1,5-dihydroxyhexylidene]amino}(methyl)amino)acetic acid (PMID: 33468467) (PMID: 31620232) (PMID: 31159660) (PMID: 29497617).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242105163D          

 37 36  0  0  0  0            999 V2000
    3.8211    1.9453   -0.0814 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5247    0.8046    0.7198 N   0  0  2  0  0  0  0  0  0  0  0  0
    4.0509   -0.4149    0.2140 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7194   -1.5712    1.0488 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0435   -1.4812    2.0962 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1678   -2.8439    0.6765 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2247    0.7626    1.1967 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2124    0.2284    0.3722 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4646   -0.2118   -0.7818 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1758    0.2072    0.9281 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1693   -0.4228   -0.0290 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1354    0.3780   -1.2469 N   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5411   -0.3172    0.5611 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6444   -0.9013   -0.2487 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.8282   -0.6923    0.5029 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8514   -0.2327   -1.5976 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.0758    1.1710   -1.4262 N   0  0  2  0  0  0  0  0  0  0  0  0
    3.3868    2.8732    0.3417 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9291    2.0878   -0.0851 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4310    1.7609   -1.1106 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7551   -0.6067   -0.8555 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1725   -0.3257    0.1783 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1275   -3.0761    0.8493 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9833    1.1124    2.1369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4431    1.2720    1.0967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1498   -0.2946    1.8978 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8858   -1.4758   -0.2203 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5697    1.2526   -1.1202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6935   -0.1597   -2.0286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7694    0.7609    0.7363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5563   -0.8317    1.5510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5269   -1.9916   -0.3377 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6168   -0.8723   -0.0696 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8129   -0.6558   -2.0210 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0473   -0.4398   -2.3045 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0812    1.4462   -1.5624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4402    1.7559   -2.0177 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
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
  1 18  1  0  0  0  0
  1 19  1  0  0  0  0
  1 20  1  0  0  0  0
  3 21  1  0  0  0  0
  3 22  1  0  0  0  0
  6 23  1  0  0  0  0
  7 24  1  0  0  0  0
 10 25  1  0  0  0  0
 10 26  1  0  0  0  0
 11 27  1  6  0  0  0
 12 28  1  0  0  0  0
 12 29  1  0  0  0  0
 13 30  1  0  0  0  0
 13 31  1  0  0  0  0
 14 32  1  6  0  0  0
 15 33  1  0  0  0  0
 16 34  1  0  0  0  0
 16 35  1  0  0  0  0
 17 36  1  0  0  0  0
 17 37  1  0  0  0  0
M  END

     RDKit          3D

 37 36  0  0  0  0  0  0  0  0999 V2000
    3.8211    1.9453   -0.0814 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5247    0.8046    0.7198 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0509   -0.4149    0.2140 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7194   -1.5712    1.0488 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0435   -1.4812    2.0962 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1678   -2.8439    0.6765 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2247    0.7626    1.1967 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2124    0.2284    0.3722 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4646   -0.2118   -0.7818 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1758    0.2072    0.9281 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1693   -0.4228   -0.0290 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1354    0.3780   -1.2469 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5411   -0.3172    0.5611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6444   -0.9013   -0.2487 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.8282   -0.6923    0.5029 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8514   -0.2327   -1.5976 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0758    1.1710   -1.4262 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3868    2.8732    0.3417 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9291    2.0878   -0.0851 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4310    1.7609   -1.1106 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7551   -0.6067   -0.8555 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1725   -0.3257    0.1783 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1275   -3.0761    0.8493 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9833    1.1124    2.1369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4431    1.2720    1.0967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1498   -0.2946    1.8978 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8858   -1.4758   -0.2203 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5697    1.2526   -1.1202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6935   -0.1597   -2.0286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7694    0.7609    0.7363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5563   -0.8317    1.5510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5269   -1.9916   -0.3377 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6168   -0.8723   -0.0696 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8129   -0.6558   -2.0210 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0473   -0.4398   -2.3045 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0812    1.4462   -1.5624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4402    1.7559   -2.0177 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
  4  5  2  0
  4  6  1  0
  2  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  3 22  1  0
  6 23  1  0
  7 24  1  0
 10 25  1  0
 10 26  1  0
 11 27  1  6
 12 28  1  0
 12 29  1  0
 13 30  1  0
 13 31  1  0
 14 32  1  6
 15 33  1  0
 16 34  1  0
 16 35  1  0
 17 36  1  0
 17 37  1  0
M  END


  Mrv1652306242105163D          

 37 36  0  0  0  0            999 V2000
    3.8211    1.9453   -0.0814 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5247    0.8046    0.7198 N   0  0  2  0  0  0  0  0  0  0  0  0
    4.0509   -0.4149    0.2140 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7194   -1.5712    1.0488 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0435   -1.4812    2.0962 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1678   -2.8439    0.6765 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2247    0.7626    1.1967 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2124    0.2284    0.3722 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4646   -0.2118   -0.7818 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1758    0.2072    0.9281 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1693   -0.4228   -0.0290 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1354    0.3780   -1.2469 N   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5411   -0.3172    0.5611 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6444   -0.9013   -0.2487 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.8282   -0.6923    0.5029 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8514   -0.2327   -1.5976 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.0758    1.1710   -1.4262 N   0  0  2  0  0  0  0  0  0  0  0  0
    3.3868    2.8732    0.3417 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9291    2.0878   -0.0851 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4310    1.7609   -1.1106 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7551   -0.6067   -0.8555 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1725   -0.3257    0.1783 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1275   -3.0761    0.8493 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9833    1.1124    2.1369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4431    1.2720    1.0967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1498   -0.2946    1.8978 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8858   -1.4758   -0.2203 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5697    1.2526   -1.1202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6935   -0.1597   -2.0286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7694    0.7609    0.7363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5563   -0.8317    1.5510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5269   -1.9916   -0.3377 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6168   -0.8723   -0.0696 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8129   -0.6558   -2.0210 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0473   -0.4398   -2.3045 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0812    1.4462   -1.5624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4402    1.7559   -2.0177 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
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
  1 18  1  0  0  0  0
  1 19  1  0  0  0  0
  1 20  1  0  0  0  0
  3 21  1  0  0  0  0
  3 22  1  0  0  0  0
  6 23  1  0  0  0  0
  7 24  1  0  0  0  0
 10 25  1  0  0  0  0
 10 26  1  0  0  0  0
 11 27  1  6  0  0  0
 12 28  1  0  0  0  0
 12 29  1  0  0  0  0
 13 30  1  0  0  0  0
 13 31  1  0  0  0  0
 14 32  1  6  0  0  0
 15 33  1  0  0  0  0
 16 34  1  0  0  0  0
 16 35  1  0  0  0  0
 17 36  1  0  0  0  0
 17 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0021548

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C9H20N4O4/c1-13(5-9(16)17)12-8(15)3-6(11)2-7(14)4-10/h6-7,14H,2-5,10-11H2,1H3,(H,12,15)(H,16,17)/t6-,7-/m1/s1

> <INCHI_KEY>
IKHFJPZQZVMLRH-RNFRBKRXSA-N

> <FORMULA>
C9H20N4O4

> <MOLECULAR_WEIGHT>
248.2795

> <EXACT_MASS>
248.148455148

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
25.05183175460641

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(3R,5R)-3,6-diamino-5-hydroxy-N'-methylhexanehydrazido]acetic acid

> <ALOGPS_LOGP>
-3.60

> <JCHEM_LOGP>
-6.230302715651079

> <ALOGPS_LOGS>
-0.99

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.479776826981986

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.016318310366975

> <JCHEM_PKA_STRONGEST_BASIC>
9.685453997096024

> <JCHEM_POLAR_SURFACE_AREA>
141.91000000000003

> <JCHEM_REFRACTIVITY>
60.1509

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.52e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(3R,5R)-3,6-diamino-5-hydroxy-N'-methylhexanehydrazido]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 37 36  0  0  0  0  0  0  0  0999 V2000
    3.8211    1.9453   -0.0814 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5247    0.8046    0.7198 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0509   -0.4149    0.2140 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7194   -1.5712    1.0488 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0435   -1.4812    2.0962 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1678   -2.8439    0.6765 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2247    0.7626    1.1967 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2124    0.2284    0.3722 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4646   -0.2118   -0.7818 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1758    0.2072    0.9281 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1693   -0.4228   -0.0290 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1354    0.3780   -1.2469 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5411   -0.3172    0.5611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6444   -0.9013   -0.2487 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.8282   -0.6923    0.5029 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8514   -0.2327   -1.5976 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0758    1.1710   -1.4262 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3868    2.8732    0.3417 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9291    2.0878   -0.0851 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4310    1.7609   -1.1106 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7551   -0.6067   -0.8555 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1725   -0.3257    0.1783 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1275   -3.0761    0.8493 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9833    1.1124    2.1369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4431    1.2720    1.0967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1498   -0.2946    1.8978 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8858   -1.4758   -0.2203 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5697    1.2526   -1.1202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6935   -0.1597   -2.0286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7694    0.7609    0.7363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5563   -0.8317    1.5510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5269   -1.9916   -0.3377 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6168   -0.8723   -0.0696 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8129   -0.6558   -2.0210 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0473   -0.4398   -2.3045 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0812    1.4462   -1.5624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4402    1.7559   -2.0177 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
  4  5  2  0
  4  6  1  0
  2  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  3 22  1  0
  6 23  1  0
  7 24  1  0
 10 25  1  0
 10 26  1  0
 11 27  1  6
 12 28  1  0
 12 29  1  0
 13 30  1  0
 13 31  1  0
 14 32  1  6
 15 33  1  0
 16 34  1  0
 16 35  1  0
 17 36  1  0
 17 37  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  C   UNK     0       3.821   1.945  -0.081  0.00  0.00           C+0
HETATM    2  N   UNK     0       3.525   0.805   0.720  0.00  0.00           N+0
HETATM    3  C   UNK     0       4.051  -0.415   0.214  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.719  -1.571   1.049  0.00  0.00           C+0
HETATM    5  O   UNK     0       3.043  -1.481   2.096  0.00  0.00           O+0
HETATM    6  O   UNK     0       4.168  -2.844   0.677  0.00  0.00           O+0
HETATM    7  N   UNK     0       2.225   0.763   1.197  0.00  0.00           N+0
HETATM    8  C   UNK     0       1.212   0.228   0.372  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.465  -0.212  -0.782  0.00  0.00           O+0
HETATM   10  C   UNK     0      -0.176   0.207   0.928  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.169  -0.423  -0.029  0.00  0.00           C+0
HETATM   12  N   UNK     0      -1.135   0.378  -1.247  0.00  0.00           N+0
HETATM   13  C   UNK     0      -2.541  -0.317   0.561  0.00  0.00           C+0
HETATM   14  C   UNK     0      -3.644  -0.901  -0.249  0.00  0.00           C+0
HETATM   15  O   UNK     0      -4.828  -0.692   0.503  0.00  0.00           O+0
HETATM   16  C   UNK     0      -3.851  -0.233  -1.598  0.00  0.00           C+0
HETATM   17  N   UNK     0      -4.076   1.171  -1.426  0.00  0.00           N+0
HETATM   18  H   UNK     0       3.387   2.873   0.342  0.00  0.00           H+0
HETATM   19  H   UNK     0       4.929   2.088  -0.085  0.00  0.00           H+0
HETATM   20  H   UNK     0       3.431   1.761  -1.111  0.00  0.00           H+0
HETATM   21  H   UNK     0       3.755  -0.607  -0.856  0.00  0.00           H+0
HETATM   22  H   UNK     0       5.173  -0.326   0.178  0.00  0.00           H+0
HETATM   23  H   UNK     0       5.128  -3.076   0.849  0.00  0.00           H+0
HETATM   24  H   UNK     0       1.983   1.112   2.137  0.00  0.00           H+0
HETATM   25  H   UNK     0      -0.443   1.272   1.097  0.00  0.00           H+0
HETATM   26  H   UNK     0      -0.150  -0.295   1.898  0.00  0.00           H+0
HETATM   27  H   UNK     0      -0.886  -1.476  -0.220  0.00  0.00           H+0
HETATM   28  H   UNK     0      -0.570   1.253  -1.120  0.00  0.00           H+0
HETATM   29  H   UNK     0      -0.694  -0.160  -2.029  0.00  0.00           H+0
HETATM   30  H   UNK     0      -2.769   0.761   0.736  0.00  0.00           H+0
HETATM   31  H   UNK     0      -2.556  -0.832   1.551  0.00  0.00           H+0
HETATM   32  H   UNK     0      -3.527  -1.992  -0.338  0.00  0.00           H+0
HETATM   33  H   UNK     0      -5.617  -0.872  -0.070  0.00  0.00           H+0
HETATM   34  H   UNK     0      -4.813  -0.656  -2.021  0.00  0.00           H+0
HETATM   35  H   UNK     0      -3.047  -0.440  -2.305  0.00  0.00           H+0
HETATM   36  H   UNK     0      -5.081   1.446  -1.562  0.00  0.00           H+0
HETATM   37  H   UNK     0      -3.440   1.756  -2.018  0.00  0.00           H+0
CONECT    1    2   18   19   20                                             
CONECT    2    1    3    7                                                  
CONECT    3    2    4   21   22                                             
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4   23                                                       
CONECT    7    2    8   24                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   25   26                                             
CONECT   11   10   12   13   27                                             
CONECT   12   11   28   29                                                  
CONECT   13   11   14   30   31                                             
CONECT   14   13   15   16   32                                             
CONECT   15   14   33                                                       
CONECT   16   14   17   34   35                                             
CONECT   17   16   36   37                                                  
CONECT   18    1                                                            
CONECT   19    1                                                            
CONECT   20    1                                                            
CONECT   21    3                                                            
CONECT   22    3                                                            
CONECT   23    6                                                            
CONECT   24    7                                                            
CONECT   25   10                                                            
CONECT   26   10                                                            
CONECT   27   11                                                            
CONECT   28   12                                                            
CONECT   29   12                                                            
CONECT   30   13                                                            
CONECT   31   13                                                            
CONECT   32   14                                                            
CONECT   33   15                                                            
CONECT   34   16                                                            
CONECT   35   16                                                            
CONECT   36   17                                                            
CONECT   37   17                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   72    0
END

RDKit          3D

37 36  0  0  0  0  0  0  0  0999 V2000
    3.8211    1.9453   -0.0814 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5247    0.8046    0.7198 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0509   -0.4149    0.2140 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7194   -1.5712    1.0488 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0435   -1.4812    2.0962 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1678   -2.8439    0.6765 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2247    0.7626    1.1967 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2124    0.2284    0.3722 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4646   -0.2118   -0.7818 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1758    0.2072    0.9281 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1693   -0.4228   -0.0290 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1354    0.3780   -1.2469 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5411   -0.3172    0.5611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6444   -0.9013   -0.2487 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.8282   -0.6923    0.5029 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8514   -0.2327   -1.5976 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0758    1.1710   -1.4262 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3868    2.8732    0.3417 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9291    2.0878   -0.0851 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4310    1.7609   -1.1106 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7551   -0.6067   -0.8555 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1725   -0.3257    0.1783 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1275   -3.0761    0.8493 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9833    1.1124    2.1369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4431    1.2720    1.0967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1498   -0.2946    1.8978 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8858   -1.4758   -0.2203 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5697    1.2526   -1.1202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6935   -0.1597   -2.0286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7694    0.7609    0.7363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5563   -0.8317    1.5510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5269   -1.9916   -0.3377 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6168   -0.8723   -0.0696 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8129   -0.6558   -2.0210 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0473   -0.4398   -2.3045 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0812    1.4462   -1.5624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4402    1.7559   -2.0177 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
  4  5  2  0
  4  6  1  0
  2  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  3 22  1  0
  6 23  1  0
  7 24  1  0
 10 25  1  0
 10 26  1  0
 11 27  1  6
 12 28  1  0
 12 29  1  0
 13 30  1  0
 13 31  1  0
 14 32  1  6
 15 33  1  0
 16 34  1  0
 16 35  1  0
 17 36  1  0
 17 37  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
2-({[(3R,5R)-3,6-diamino-1,5-dihydroxyhexylidene]amino}(methyl)amino)acetate	Generator
(2-((3R,5R)-3,6-diamino-5-Hydroxyhexanoyl)-1-methylhydrazino) acetic acid	MeSH
Negamycin, (threo-D)-isomer	MeSH

Chemical Formula

C₉H₂₀N₄O₄

Average Mass

248.2795 Da

Monoisotopic Mass

248.14846 Da

IUPAC Name

2-[(3R,5R)-3,6-diamino-5-hydroxy-N'-methylhexanehydrazido]acetic acid

Traditional Name

[(3R,5R)-3,6-diamino-5-hydroxy-N'-methylhexanehydrazido]acetic acid

CAS Registry Number

Not Available

SMILES

CN(CC(O)=O)NC(=O)C[C@H](N)C[C@@H](O)CN

InChI Identifier

InChI=1S/C9H20N4O4/c1-13(5-9(16)17)12-8(15)3-6(11)2-7(14)4-10/h6-7,14H,2-5,10-11H2,1H3,(H,12,15)(H,16,17)/t6-,7-/m1/s1

InChI Key

IKHFJPZQZVMLRH-RNFRBKRXSA-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
Streptomyces	NPAtlas	5121145
Streptomyces No. M890-C2	Bacteria	KNApSAcK

Species Where Detected

Species Name	Source	Reference
Streptomyces goshikiensis No.MD967-A2	KNApSAcK Database	22123792

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as beta amino acids and derivatives. These are amino acids having a (-NH2) group attached to the beta carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Beta amino acids and derivatives

Alternative Parents

Substituents

Beta amino acid or derivatives
Alpha-amino acid or derivatives
1,3-aminoalcohol
1,2-aminoalcohol
Amino acid
Secondary alcohol
Carboxylic acid hydrazide
Carboxylic acid
Monocarboxylic acid or derivatives
Organic nitrogen compound
Organonitrogen compound
Primary aliphatic amine
Organooxygen compound
Primary amine
Carbonyl group
Hydrocarbon derivative
Amine
Organic oxide
Alcohol
Organic oxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

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	-3.6	ALOGPS
logP	-6.2	ChemAxon
logS	-0.99	ALOGPS
pKa (Strongest Acidic)	4.02	ChemAxon
pKa (Strongest Basic)	9.69	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	141.91 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	60.15 m³·mol⁻¹	ChemAxon
Polarizability	25.05 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA000890

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

9293543

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11118411

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Kondo S, Shibahara S, Takahashi S, Maeda K, Umezawa H: Negamycin, a novel hydrazide antibiotic. J Am Chem Soc. 1971 Nov;93(23):6305-6. doi: 10.1021/ja00752a072. [PubMed:5121145 ]
Horompoli D, Ciglia C, Glusenkamp KH, Haustedt LO, Falkenstein-Paul H, Bendas G, Berscheid A, Brotz-Oesterhelt H: The Antibiotic Negamycin Crosses the Bacterial Cytoplasmic Membrane by Multiple Routes. Antimicrob Agents Chemother. 2021 Mar 18;65(4). pii: AAC.00986-20. doi: 10.1128/AAC.00986-20. Print 2021 Mar 18. [PubMed:33468467 ]
Hamada K, Omura N, Taguchi A, Baradaran-Heravi A, Kotake M, Arai M, Takayama K, Taniguchi A, Roberge M, Hayashi Y: New Negamycin-Based Potent Readthrough Derivative Effective against TGA-Type Nonsense Mutations. ACS Med Chem Lett. 2019 Sep 23;10(10):1450-1456. doi: 10.1021/acsmedchemlett.9b00273. eCollection 2019 Oct 10. [PubMed:31620232 ]
Hamada K, Naito A, Hamaguchi Y, Kanesaki Y, Kasahara K, Taguchi A, Omura N, Hayashi Y, Usui T: Ubr1p-Cup9p-Ptr2p pathway involves in the sensitivity to readthrough compounds negamycin derivatives in budding yeast. Biosci Biotechnol Biochem. 2019 Oct;83(10):1889-1892. doi: 10.1080/09168451.2019.1625263. Epub 2019 Jun 4. [PubMed:31159660 ]
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Showing NP-Card for Negamycin (NP0021548)

MOL for NP0021548 (Negamycin)

3D MOL for NP0021548 (Negamycin)

3D SDF for NP0021548 (Negamycin)

3D-SDF for NP0021548 (Negamycin)

PDB for NP0021548 (Negamycin)

3D PDB for NP0021548 (Negamycin)

SMILES for NP0021548 (Negamycin)

INCHI for NP0021548 (Negamycin)

Structure for NP0021548 (Negamycin)

3D Structure for NP0021548 (Negamycin)