NP-MRD: Showing NP-Card for Rhodopeptin B5 (NP0003083)

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Record Information

Version

1.0

Created at

2020-12-09 00:10:48 UTC

Updated at

2021-07-15 16:45:28 UTC

NP-MRD ID

NP0003083

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Rhodopeptin B5

Provided By

NPAtlas

Description

Rhodopeptin B5 is found in Rhodococcus. It was first documented in 1999 (PMID: 10580383). Based on a literature review very few articles have been published on (3S,6S,13R)-6-(4-aminobutyl)-13-(10-methylundecyl)-3-(propan-2-yl)-1,4,7,10-tetraazacyclotrideca-1,4,7,10-tetraene-2,5,8,11-tetrol.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652307012117063D          

 90 90  0  0  0  0            999 V2000
    9.5187    1.7158   -0.1807 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.8520   -1.1380    0.0025 C   0  0  2  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

 90 90  0  0  0  0  0  0  0  0999 V2000
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   -0.2323   -0.2244   -1.1737 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8264   -0.0476    0.2340 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1029   -2.4172    0.4148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5945   -2.6262   -2.0356 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7004   -3.6414   -1.3379 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9328   -5.0260   -1.1718 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1494   -3.9126    0.6334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3557   -2.3850    0.3107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4793   -1.8878   -1.3287 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7790   -0.6521   -2.8304 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.4837    3.1767   -1.7765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7034    3.9852   -0.7578 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.3650   -0.2784    2.9146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2200   -1.6563    2.8108 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.9267    1.6801    2.9546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1907    2.2640    3.1776 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9496    2.2595    1.5363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1671   -2.8760    1.3410 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  2  0
 19 21  1  0
 21 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  1  0
 22 28  1  0
 28 29  2  0
 28 30  1  0
 30 31  1  0
 31 32  1  0
 32 33  1  0
 32 34  1  0
 31 35  1  0
 35 36  2  0
 35 37  1  0
 37 13  1  0
  1 38  1  0
  1 39  1  0
  1 40  1  0
  2 41  1  6
  3 42  1  0
  3 43  1  0
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  4 45  1  0
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  5 47  1  0
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  7 51  1  0
  7 52  1  0
  8 53  1  0
  8 54  1  0
  9 55  1  0
  9 56  1  0
 10 57  1  0
 10 58  1  0
 11 59  1  0
 11 60  1  0
 12 61  1  0
 12 62  1  0
 13 63  1  1
 14 64  1  0
 14 65  1  0
 17 66  1  0
 18 67  1  0
 18 68  1  0
 21 69  1  0
 22 70  1  6
 23 71  1  0
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 27 79  1  0
 27 80  1  0
 30 81  1  0
 31 82  1  1
 32 83  1  1
 33 84  1  0
 33 85  1  0
 33 86  1  0
 34 87  1  0
 34 88  1  0
 34 89  1  0
 37 90  1  0
M  END


  Mrv1652307012117063D          

 90 90  0  0  0  0            999 V2000
    9.5187    1.7158   -0.1807 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3230    2.3454   -0.8432 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.7073    3.7522   -1.2522 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1360    2.4487    0.0856 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.6892    1.0939    0.5849 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.2819    0.1826   -0.5531 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.8520   -1.1380    0.0025 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6900   -1.0475    0.9420 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4565   -0.4741    0.3280 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0111   -1.3232   -0.8328 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7711   -0.8018   -1.4987 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5753   -0.7070   -0.6386 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1264   -2.0115   -0.0475 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2384   -3.0633   -1.0656 C   0  0  1  0  0  0  0  0  0  0  0  0
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   -0.8627   -1.8877    0.9936 N   0  0  0  0  0  0  0  0  0  0  0  0
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   10.1154    2.4653    0.4143 H   0  0  0  0  0  0  0  0  0  0  0  0
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    8.5487    4.4960   -0.4641 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1410    4.0881   -2.1487 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.7888    3.8156   -1.5312 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3364    2.9603   -0.4497 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4375    3.0461    0.9555 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4406    0.6447    1.2393 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7750    1.2719    1.1968 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4720    0.6086   -1.1490 H   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
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  6  7  1  0  0  0  0
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 17 18  1  0  0  0  0
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 31 32  1  0  0  0  0
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 31 35  1  0  0  0  0
 35 36  2  0  0  0  0
 35 37  1  0  0  0  0
 37 13  1  0  0  0  0
  1 38  1  0  0  0  0
  1 39  1  0  0  0  0
  1 40  1  0  0  0  0
  2 41  1  6  0  0  0
  3 42  1  0  0  0  0
  3 43  1  0  0  0  0
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  5 48  1  0  0  0  0
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  6 50  1  0  0  0  0
  7 51  1  0  0  0  0
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  8 53  1  0  0  0  0
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  9 55  1  0  0  0  0
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 13 63  1  1  0  0  0
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 14 65  1  0  0  0  0
 17 66  1  0  0  0  0
 18 67  1  0  0  0  0
 18 68  1  0  0  0  0
 21 69  1  0  0  0  0
 22 70  1  6  0  0  0
 23 71  1  0  0  0  0
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 30 81  1  0  0  0  0
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 34 87  1  0  0  0  0
 34 88  1  0  0  0  0
 34 89  1  0  0  0  0
 37 90  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0003083

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]N([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[C@]1([H])N([H])C(=O)C([H])([H])N([H])C(=O)C([H])([H])[C@]([H])(N([H])C(=O)[C@@]([H])(N([H])C1=O)C([H])(C([H])([H])[H])C([H])([H])[H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])(C([H])([H])[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C28H53N5O4/c1-20(2)14-10-8-6-5-7-9-11-15-22-18-24(34)30-19-25(35)32-23(16-12-13-17-29)27(36)33-26(21(3)4)28(37)31-22/h20-23,26H,5-19,29H2,1-4H3,(H,30,34)(H,31,37)(H,32,35)(H,33,36)/t22-,23+,26+/m1/s1

> <INCHI_KEY>
CQVSTNLAGJAEKO-UMFSSWHCSA-N

> <FORMULA>
C28H53N5O4

> <MOLECULAR_WEIGHT>
523.763

> <EXACT_MASS>
523.409755207

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
90

> <JCHEM_AVERAGE_POLARIZABILITY>
60.95160483896454

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,13R)-6-(4-aminobutyl)-13-(10-methylundecyl)-3-(propan-2-yl)-1,4,7,10-tetraazacyclotridecane-2,5,8,11-tetrone

> <ALOGPS_LOGP>
3.24

> <JCHEM_LOGP>
2.627775936429114

> <ALOGPS_LOGS>
-4.98

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.00168518718563

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.157968679110471

> <JCHEM_PKA_STRONGEST_BASIC>
10.126247192244687

> <JCHEM_POLAR_SURFACE_AREA>
142.42

> <JCHEM_REFRACTIVITY>
146.1094

> <JCHEM_ROTATABLE_BOND_COUNT>
15

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.49e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,13R)-6-(4-aminobutyl)-3-isopropyl-13-(10-methylundecyl)-1,4,7,10-tetraazacyclotridecane-2,5,8,11-tetrone

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 90 90  0  0  0  0  0  0  0  0999 V2000
    9.5187    1.7158   -0.1807 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3230    2.3454   -0.8432 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.7073    3.7522   -1.2522 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1360    2.4487    0.0856 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6892    1.0939    0.5849 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2819    0.1826   -0.5531 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8520   -1.1380    0.0025 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6900   -1.0475    0.9420 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4565   -0.4741    0.3280 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0111   -1.3232   -0.8328 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7711   -0.8018   -1.4987 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5753   -0.7070   -0.6386 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1264   -2.0115   -0.0475 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2384   -3.0633   -1.0656 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1846   -4.0253   -0.4835 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6081   -4.8891    0.3027 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5735   -4.1508   -0.6453 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6305   -3.2983   -0.1881 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7381   -3.0881   -1.1729 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0555   -4.1062   -1.8522 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.8493   -0.5704   -1.6309 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.8150    0.5449   -1.5474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5270    0.7731   -0.2606 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5221    1.9262   -0.3679 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8828    3.2234   -0.7400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8915    3.7030    0.1744 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4778   -0.3758   -1.1710 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6722   -1.0703   -1.9724 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.4333    0.2254    1.1615 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4613    0.3142    2.2479 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.5256   -0.7021    2.2850 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9074    1.7423    2.5202 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4505   -0.7914    1.6043 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0763   -0.5944    2.8320 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8627   -1.8877    0.9936 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.2179    1.4000   -1.0065 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.1154    2.4653    0.4143 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2955    0.8260    0.4058 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0783    1.8006   -1.7807 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5487    4.4960   -0.4641 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1410    4.0881   -2.1487 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.7888    3.8156   -1.5312 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3364    2.9603   -0.4497 H   0  0  0  0  0  0  0  0  0  0  0  0
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    5.7750    1.2719    1.1968 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4720    0.6086   -1.1490 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1312   -0.0073   -1.2459 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7195   -1.5307    0.6071 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7012   -1.8968   -0.7957 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0083   -0.5043    1.8421 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4606   -2.0913    1.2769 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6812   -0.4124    1.1208 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6426    0.5643   -0.0109 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8241   -1.2746   -1.5902 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9399   -2.3791   -0.5283 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5950   -1.4359   -2.3993 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0072    0.2098   -1.8900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2323   -0.2244   -1.1737 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8264   -0.0476    0.2340 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1029   -2.4172    0.4148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5945   -2.6262   -2.0356 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7004   -3.6414   -1.3379 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9328   -5.0260   -1.1718 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1494   -3.9126    0.6334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3557   -2.3850    0.3107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4793   -1.8878   -1.3287 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7790   -0.6521   -2.8304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2313    1.4902   -1.7771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5965    0.5274   -2.3449 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.0746   -0.0915    0.1217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9712    2.0368    0.6576 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.4837    3.1767   -1.7765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7034    3.9852   -0.7578 H   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0
  2  3  1  0
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  4  5  1  0
  5  6  1  0
  6  7  1  0
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  9 10  1  0
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 35 36  2  0
 35 37  1  0
 37 13  1  0
  1 38  1  0
  1 39  1  0
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 37 90  1  0
M  END

HEADER    PROTEIN                                 01-JUL-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   01-JUL-21         0                                  
HETATM    1  C   UNK     0       9.519   1.716  -0.181  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.323   2.345  -0.843  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.707   3.752  -1.252  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.136   2.449   0.086  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.689   1.094   0.585  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.282   0.183  -0.553  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.852  -1.138   0.003  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.690  -1.048   0.942  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.457  -0.474   0.328  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.011  -1.323  -0.833  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.771  -0.802  -1.499  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.575  -0.707  -0.639  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.126  -2.011  -0.048  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.238  -3.063  -1.066  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.185  -4.025  -0.484  0.00  0.00           C+0
HETATM   16  O   UNK     0      -0.608  -4.889   0.303  0.00  0.00           O+0
HETATM   17  N   UNK     0      -2.574  -4.151  -0.645  0.00  0.00           N+0
HETATM   18  C   UNK     0      -3.631  -3.298  -0.188  0.00  0.00           C+0
HETATM   19  C   UNK     0      -4.738  -3.088  -1.173  0.00  0.00           C+0
HETATM   20  O   UNK     0      -5.056  -4.106  -1.852  0.00  0.00           O+0
HETATM   21  N   UNK     0      -5.411  -1.877  -1.368  0.00  0.00           N+0
HETATM   22  C   UNK     0      -4.849  -0.570  -1.631  0.00  0.00           C+0
HETATM   23  C   UNK     0      -5.815   0.545  -1.547  0.00  0.00           C+0
HETATM   24  C   UNK     0      -6.527   0.773  -0.261  0.00  0.00           C+0
HETATM   25  C   UNK     0      -7.522   1.926  -0.368  0.00  0.00           C+0
HETATM   26  C   UNK     0      -6.883   3.223  -0.740  0.00  0.00           C+0
HETATM   27  N   UNK     0      -5.891   3.703   0.174  0.00  0.00           N+0
HETATM   28  C   UNK     0      -3.478  -0.376  -1.171  0.00  0.00           C+0
HETATM   29  O   UNK     0      -2.672  -1.070  -1.972  0.00  0.00           O+0
HETATM   30  N   UNK     0      -2.788   0.295  -0.187  0.00  0.00           N+0
HETATM   31  C   UNK     0      -2.433   0.225   1.161  0.00  0.00           C+0
HETATM   32  C   UNK     0      -3.461   0.314   2.248  0.00  0.00           C+0
HETATM   33  C   UNK     0      -4.526  -0.702   2.285  0.00  0.00           C+0
HETATM   34  C   UNK     0      -3.907   1.742   2.520  0.00  0.00           C+0
HETATM   35  C   UNK     0      -1.450  -0.791   1.604  0.00  0.00           C+0
HETATM   36  O   UNK     0      -1.076  -0.594   2.832  0.00  0.00           O+0
HETATM   37  N   UNK     0      -0.863  -1.888   0.994  0.00  0.00           N+0
HETATM   38  H   UNK     0      10.218   1.400  -1.006  0.00  0.00           H+0
HETATM   39  H   UNK     0      10.115   2.465   0.414  0.00  0.00           H+0
HETATM   40  H   UNK     0       9.296   0.826   0.406  0.00  0.00           H+0
HETATM   41  H   UNK     0       8.078   1.801  -1.781  0.00  0.00           H+0
HETATM   42  H   UNK     0       8.549   4.496  -0.464  0.00  0.00           H+0
HETATM   43  H   UNK     0       8.141   4.088  -2.149  0.00  0.00           H+0
HETATM   44  H   UNK     0       9.789   3.816  -1.531  0.00  0.00           H+0
HETATM   45  H   UNK     0       6.336   2.960  -0.450  0.00  0.00           H+0
HETATM   46  H   UNK     0       7.438   3.046   0.956  0.00  0.00           H+0
HETATM   47  H   UNK     0       7.441   0.645   1.239  0.00  0.00           H+0
HETATM   48  H   UNK     0       5.775   1.272   1.197  0.00  0.00           H+0
HETATM   49  H   UNK     0       5.472   0.609  -1.149  0.00  0.00           H+0
HETATM   50  H   UNK     0       7.131  -0.007  -1.246  0.00  0.00           H+0
HETATM   51  H   UNK     0       6.720  -1.531   0.607  0.00  0.00           H+0
HETATM   52  H   UNK     0       5.701  -1.897  -0.796  0.00  0.00           H+0
HETATM   53  H   UNK     0       5.008  -0.504   1.842  0.00  0.00           H+0
HETATM   54  H   UNK     0       4.461  -2.091   1.277  0.00  0.00           H+0
HETATM   55  H   UNK     0       2.681  -0.412   1.121  0.00  0.00           H+0
HETATM   56  H   UNK     0       3.643   0.564  -0.011  0.00  0.00           H+0
HETATM   57  H   UNK     0       3.824  -1.275  -1.590  0.00  0.00           H+0
HETATM   58  H   UNK     0       2.940  -2.379  -0.528  0.00  0.00           H+0
HETATM   59  H   UNK     0       1.595  -1.436  -2.399  0.00  0.00           H+0
HETATM   60  H   UNK     0       2.007   0.210  -1.890  0.00  0.00           H+0
HETATM   61  H   UNK     0      -0.232  -0.224  -1.174  0.00  0.00           H+0
HETATM   62  H   UNK     0       0.826  -0.048   0.234  0.00  0.00           H+0
HETATM   63  H   UNK     0       1.103  -2.417   0.415  0.00  0.00           H+0
HETATM   64  H   UNK     0      -0.595  -2.626  -2.036  0.00  0.00           H+0
HETATM   65  H   UNK     0       0.700  -3.641  -1.338  0.00  0.00           H+0
HETATM   66  H   UNK     0      -2.933  -5.026  -1.172  0.00  0.00           H+0
HETATM   67  H   UNK     0      -4.149  -3.913   0.633  0.00  0.00           H+0
HETATM   68  H   UNK     0      -3.356  -2.385   0.311  0.00  0.00           H+0
HETATM   69  H   UNK     0      -6.479  -1.888  -1.329  0.00  0.00           H+0
HETATM   70  H   UNK     0      -4.779  -0.652  -2.830  0.00  0.00           H+0
HETATM   71  H   UNK     0      -5.231   1.490  -1.777  0.00  0.00           H+0
HETATM   72  H   UNK     0      -6.596   0.527  -2.345  0.00  0.00           H+0
HETATM   73  H   UNK     0      -5.824   1.105   0.546  0.00  0.00           H+0
HETATM   74  H   UNK     0      -7.075  -0.092   0.122  0.00  0.00           H+0
HETATM   75  H   UNK     0      -7.971   2.037   0.658  0.00  0.00           H+0
HETATM   76  H   UNK     0      -8.336   1.719  -1.066  0.00  0.00           H+0
HETATM   77  H   UNK     0      -6.484   3.177  -1.777  0.00  0.00           H+0
HETATM   78  H   UNK     0      -7.703   3.985  -0.758  0.00  0.00           H+0
HETATM   79  H   UNK     0      -6.029   3.393   1.149  0.00  0.00           H+0
HETATM   80  H   UNK     0      -4.934   3.618  -0.193  0.00  0.00           H+0
HETATM   81  H   UNK     0      -2.336   1.217  -0.634  0.00  0.00           H+0
HETATM   82  H   UNK     0      -1.840   1.215   1.380  0.00  0.00           H+0
HETATM   83  H   UNK     0      -2.859   0.096   3.199  0.00  0.00           H+0
HETATM   84  H   UNK     0      -5.365  -0.278   2.915  0.00  0.00           H+0
HETATM   85  H   UNK     0      -4.220  -1.656   2.811  0.00  0.00           H+0
HETATM   86  H   UNK     0      -4.984  -1.018   1.358  0.00  0.00           H+0
HETATM   87  H   UNK     0      -4.927   1.680   2.955  0.00  0.00           H+0
HETATM   88  H   UNK     0      -3.191   2.264   3.178  0.00  0.00           H+0
HETATM   89  H   UNK     0      -3.950   2.260   1.536  0.00  0.00           H+0
HETATM   90  H   UNK     0      -1.167  -2.876   1.341  0.00  0.00           H+0
CONECT    1    2   38   39   40                                             
CONECT    2    1    3    4   41                                             
CONECT    3    2   42   43   44                                             
CONECT    4    2    5   45   46                                             
CONECT    5    4    6   47   48                                             
CONECT    6    5    7   49   50                                             
CONECT    7    6    8   51   52                                             
CONECT    8    7    9   53   54                                             
CONECT    9    8   10   55   56                                             
CONECT   10    9   11   57   58                                             
CONECT   11   10   12   59   60                                             
CONECT   12   11   13   61   62                                             
CONECT   13   12   14   37   63                                             
CONECT   14   13   15   64   65                                             
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   66                                                  
CONECT   18   17   19   67   68                                             
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   69                                                  
CONECT   22   21   23   28   70                                             
CONECT   23   22   24   71   72                                             
CONECT   24   23   25   73   74                                             
CONECT   25   24   26   75   76                                             
CONECT   26   25   27   77   78                                             
CONECT   27   26   79   80                                                  
CONECT   28   22   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31   81                                                  
CONECT   31   30   32   35   82                                             
CONECT   32   31   33   34   83                                             
CONECT   33   32   84   85   86                                             
CONECT   34   32   87   88   89                                             
CONECT   35   31   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   13   90                                                  
CONECT   38    1                                                            
CONECT   39    1                                                            
CONECT   40    1                                                            
CONECT   41    2                                                            
CONECT   42    3                                                            
CONECT   43    3                                                            
CONECT   44    3                                                            
CONECT   45    4                                                            
CONECT   46    4                                                            
CONECT   47    5                                                            
CONECT   48    5                                                            
CONECT   49    6                                                            
CONECT   50    6                                                            
CONECT   51    7                                                            
CONECT   52    7                                                            
CONECT   53    8                                                            
CONECT   54    8                                                            
CONECT   55    9                                                            
CONECT   56    9                                                            
CONECT   57   10                                                            
CONECT   58   10                                                            
CONECT   59   11                                                            
CONECT   60   11                                                            
CONECT   61   12                                                            
CONECT   62   12                                                            
CONECT   63   13                                                            
CONECT   64   14                                                            
CONECT   65   14                                                            
CONECT   66   17                                                            
CONECT   67   18                                                            
CONECT   68   18                                                            
CONECT   69   21                                                            
CONECT   70   22                                                            
CONECT   71   23                                                            
CONECT   72   23                                                            
CONECT   73   24                                                            
CONECT   74   24                                                            
CONECT   75   25                                                            
CONECT   76   25                                                            
CONECT   77   26                                                            
CONECT   78   26                                                            
CONECT   79   27                                                            
CONECT   80   27                                                            
CONECT   81   30                                                            
CONECT   82   31                                                            
CONECT   83   32                                                            
CONECT   84   33                                                            
CONECT   85   33                                                            
CONECT   86   33                                                            
CONECT   87   34                                                            
CONECT   88   34                                                            
CONECT   89   34                                                            
CONECT   90   37                                                            
MASTER        0    0    0    0    0    0    0    0   90    0  180    0
END

RDKit          3D

90 90  0  0  0  0  0  0  0  0999 V2000
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  1  2  1  0
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  1 38  1  0
  1 39  1  0
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  2 41  1  6
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 34 88  1  0
 34 89  1  0
 37 90  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Not Available

Chemical Formula

C₂₈H₅₃N₅O₄

Average Mass

523.7630 Da

Monoisotopic Mass

523.40976 Da

IUPAC Name

(3S,13R)-6-(4-aminobutyl)-13-(10-methylundecyl)-3-(propan-2-yl)-1,4,7,10-tetraazacyclotridecane-2,5,8,11-tetrone

Traditional Name

(3S,13R)-6-(4-aminobutyl)-3-isopropyl-13-(10-methylundecyl)-1,4,7,10-tetraazacyclotridecane-2,5,8,11-tetrone

CAS Registry Number

Not Available

SMILES

CC(C)CCCCCCCCC[C@@H]1CC(=O)NCC(=O)N[C@@H](CCCCN)C(=O)N[C@@H](C(C)C)C(=O)N1

InChI Identifier

InChI=1S/C28H53N5O4/c1-20(2)14-10-8-6-5-7-9-11-15-22-18-24(34)30-19-25(35)32-23(16-12-13-17-29)27(36)33-26(21(3)4)28(37)31-22/h20-23,26H,5-19,29H2,1-4H3,(H,30,34)(H,31,37)(H,32,35)(H,33,36)/t22-,23+,26+/m1/s1

InChI Key

CQVSTNLAGJAEKO-UMFSSWHCSA-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
Rhodococcus	NPAtlas	10580383

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	3.24	ALOGPS
logP	2.63	ChemAxon
logS	-5	ALOGPS
pKa (Strongest Acidic)	11.16	ChemAxon
pKa (Strongest Basic)	10.13	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	142.42 Å²	ChemAxon
Rotatable Bond Count	15	ChemAxon
Refractivity	146.11 m³·mol⁻¹	ChemAxon
Polarizability	60.95 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA017714

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

78438396

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139588031

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Chiba H, Agematu H, Dobashi K, Yoshioka T: Rhodopeptins, novel cyclic tetrapeptides with antifungal activities from Rhodococcus sp. II. Structure elucidation. J Antibiot (Tokyo). 1999 Aug;52(8):700-9. doi: 10.7164/antibiotics.52.700. [PubMed:10580383 ]

Showing NP-Card for Rhodopeptin B5 (NP0003083)

MOL for NP0003083 (Rhodopeptin B5)

3D MOL for NP0003083 (Rhodopeptin B5)

3D SDF for NP0003083 (Rhodopeptin B5)

3D-SDF for NP0003083 (Rhodopeptin B5)

PDB for NP0003083 (Rhodopeptin B5)

3D PDB for NP0003083 (Rhodopeptin B5)

SMILES for NP0003083 (Rhodopeptin B5)

INCHI for NP0003083 (Rhodopeptin B5)

Structure for NP0003083 (Rhodopeptin B5)

3D Structure for NP0003083 (Rhodopeptin B5)