NP-MRD: Showing NP-Card for Lynamicin D (NP0008032)

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Record Information

Version

1.0

Created at

2020-12-09 05:39:22 UTC

Updated at

2021-07-15 16:59:14 UTC

NP-MRD ID

NP0008032

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Lynamicin D

Provided By

NPAtlas

Description

2,5-Dimethyl 3,4-bis(5-chloro-1H-indol-3-yl)-1H-pyrrole-2,5-dicarboxylate belongs to the class of organic compounds known as indoles. Indoles are compounds containing an indole moiety, which consists of pyrrole ring fused to benzene to form 2,3-benzopyrrole. Lynamicin D is found in Actinomyces and Marinispora sp.. It was first documented in 2008 (PMID: 18842058). Based on a literature review very few articles have been published on 2,5-dimethyl 3,4-bis(5-chloro-1H-indol-3-yl)-1H-pyrrole-2,5-dicarboxylate.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242106063D          

 50 54  0  0  0  0            999 V2000
    2.9124    5.1487   -1.8951 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8822    4.4500   -1.2201 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7823    3.0683   -1.1916 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6655    2.4259   -1.8059 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6852    2.4362   -0.4691 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3126    3.0186    0.2203 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1342    2.0964    0.7498 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3258    2.3205    1.5598 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6514    3.5073    1.8105 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0913    1.2920    2.0494 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2484    1.5106    2.8361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6507    0.8354    0.3892 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2124   -0.4605    0.7315 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3531   -0.9511    2.0070 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9076   -2.1733    1.9615 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1385   -2.5051    0.6804 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6925   -3.6503    0.1144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8123   -3.7181   -1.2757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3810   -2.6590   -2.0150 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.8287   -1.5138   -1.4772 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.4785    1.0678   -0.3668 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3494    0.0756   -0.9775 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6483   -0.1745   -2.2857 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.8053   -1.6529   -1.1082 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5999   -2.6436   -0.5905 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6718   -2.8400    0.7701 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9564   -2.0572    1.6506 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1016   -2.3693    3.3612 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.1645   -1.0684    1.1166 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0902   -0.8683   -0.2546 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.6027   -0.4546    1.8118 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
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  6 37  1  0  0  0  0
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 28 48  1  0  0  0  0
 29 49  1  0  0  0  0
 32 50  1  0  0  0  0
M  END

     RDKit          3D

 50 54  0  0  0  0  0  0  0  0999 V2000
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    1.8822    4.4500   -1.2201 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.1385   -2.5051    0.6804 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1652306242106063D          

 50 54  0  0  0  0            999 V2000
    2.9124    5.1487   -1.8951 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8822    4.4500   -1.2201 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7823    3.0683   -1.1916 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6655    2.4259   -1.8059 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.9246   -1.6243   -3.2130 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1540   -3.2492   -1.2899 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2989   -3.6211    1.1668 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6027   -0.4546    1.8118 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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  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
  7 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  2  0  0  0  0
 12 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 30 32  1  0  0  0  0
 32 33  2  0  0  0  0
 23  5  2  0  0  0  0
 33 24  1  0  0  0  0
 22 13  1  0  0  0  0
 33 27  1  0  0  0  0
 22 16  1  0  0  0  0
  1 34  1  0  0  0  0
  1 35  1  0  0  0  0
  1 36  1  0  0  0  0
  6 37  1  0  0  0  0
 11 38  1  0  0  0  0
 11 39  1  0  0  0  0
 11 40  1  0  0  0  0
 14 41  1  0  0  0  0
 15 42  1  0  0  0  0
 17 43  1  0  0  0  0
 18 44  1  0  0  0  0
 21 45  1  0  0  0  0
 25 46  1  0  0  0  0
 26 47  1  0  0  0  0
 28 48  1  0  0  0  0
 29 49  1  0  0  0  0
 32 50  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0008032

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]N1C([H])=C(C2=C([H])C(Cl)=C([H])C([H])=C12)C1=C(N([H])C(C(=O)OC([H])([H])[H])=C1C1=C([H])N([H])C2=C([H])C([H])=C(Cl)C([H])=C12)C(=O)OC([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C24H17Cl2N3O4/c1-32-23(30)21-19(15-9-27-17-5-3-11(25)7-13(15)17)20(22(29-21)24(31)33-2)16-10-28-18-6-4-12(26)8-14(16)18/h3-10,27-29H,1-2H3

> <INCHI_KEY>
YYBKJQDTRQASSS-UHFFFAOYSA-N

> <FORMULA>
C24H17Cl2N3O4

> <MOLECULAR_WEIGHT>
482.32

> <EXACT_MASS>
481.0596114

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
50

> <JCHEM_AVERAGE_POLARIZABILITY>
47.99382587273147

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,5-dimethyl 3,4-bis(5-chloro-1H-indol-3-yl)-1H-pyrrole-2,5-dicarboxylate

> <ALOGPS_LOGP>
5.09

> <JCHEM_LOGP>
5.6001501666666655

> <ALOGPS_LOGS>
-6.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.120905546449286

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.206934080204427

> <JCHEM_PKA_STRONGEST_BASIC>
-6.838668855370437

> <JCHEM_POLAR_SURFACE_AREA>
99.97

> <JCHEM_REFRACTIVITY>
126.67739999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.70e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
lynamicin D

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 50 54  0  0  0  0  0  0  0  0999 V2000
    2.9124    5.1487   -1.8951 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8822    4.4500   -1.2201 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7823    3.0683   -1.1916 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6655    2.4259   -1.8059 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6852    2.4362   -0.4691 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3126    3.0186    0.2203 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1342    2.0964    0.7498 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3258    2.3205    1.5598 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6514    3.5073    1.8105 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0913    1.2920    2.0494 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2484    1.5106    2.8361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6507    0.8354    0.3892 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2124   -0.4605    0.7315 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3531   -0.9511    2.0070 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9076   -2.1733    1.9615 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1385   -2.5051    0.6804 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6925   -3.6503    0.1144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8123   -3.7181   -1.2757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3810   -2.6590   -2.0150 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5112   -2.6952   -3.7801 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.8287   -1.5138   -1.4772 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7092   -1.4461   -0.0910 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4785    1.0678   -0.3668 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3494    0.0756   -0.9775 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6483   -0.1745   -2.2857 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5156   -1.2052   -2.3544 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8053   -1.6529   -1.1082 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5999   -2.6436   -0.5905 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6718   -2.8400    0.7701 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9564   -2.0572    1.6506 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1016   -2.3693    3.3612 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.1645   -1.0684    1.1166 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0902   -0.8683   -0.2546 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9135    4.8645   -1.5103 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7048    6.2311   -1.7772 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8620    4.9381   -2.9858 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4146    4.0729    0.3179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9510    1.6475    3.9054 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9729    0.6950    2.7049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7694    2.4538    2.5524 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0464   -0.3964    2.9062 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1290   -2.7765    2.7634 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0223   -4.4659    0.7269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2448   -4.6115   -1.7094 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4963   -0.6904   -2.0970 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2376    0.3851   -3.1230 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9246   -1.6243   -3.2130 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1540   -3.2492   -1.2899 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2989   -3.6211    1.1668 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6027   -0.4546    1.8118 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  1  0
  7 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 19 21  1  0
 21 22  2  0
 12 23  1  0
 23 24  1  0
 24 25  2  0
 25 26  1  0
 26 27  1  0
 27 28  2  0
 28 29  1  0
 29 30  2  0
 30 31  1  0
 30 32  1  0
 32 33  2  0
 23  5  2  0
 33 24  1  0
 22 13  1  0
 33 27  1  0
 22 16  1  0
  1 34  1  0
  1 35  1  0
  1 36  1  0
  6 37  1  0
 11 38  1  0
 11 39  1  0
 11 40  1  0
 14 41  1  0
 15 42  1  0
 17 43  1  0
 18 44  1  0
 21 45  1  0
 25 46  1  0
 26 47  1  0
 28 48  1  0
 29 49  1  0
 32 50  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       2.912   5.149  -1.895  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.882   4.450  -1.220  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.782   3.068  -1.192  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.666   2.426  -1.806  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.685   2.436  -0.469  0.00  0.00           C+0
HETATM    6  N   UNK     0      -0.313   3.019   0.220  0.00  0.00           N+0
HETATM    7  C   UNK     0      -1.134   2.096   0.750  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.326   2.321   1.560  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.651   3.507   1.811  0.00  0.00           O+0
HETATM   10  O   UNK     0      -3.091   1.292   2.049  0.00  0.00           O+0
HETATM   11  C   UNK     0      -4.248   1.511   2.836  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.651   0.835   0.389  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.212  -0.461   0.732  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.353  -0.951   2.007  0.00  0.00           C+0
HETATM   15  N   UNK     0      -1.908  -2.173   1.962  0.00  0.00           N+0
HETATM   16  C   UNK     0      -2.139  -2.505   0.680  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.692  -3.650   0.114  0.00  0.00           C+0
HETATM   18  C   UNK     0      -2.812  -3.718  -1.276  0.00  0.00           C+0
HETATM   19  C   UNK     0      -2.381  -2.659  -2.015  0.00  0.00           C+0
HETATM   20 Cl   UNK     0      -2.511  -2.695  -3.780  0.00  0.00          Cl+0
HETATM   21  C   UNK     0      -1.829  -1.514  -1.477  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.709  -1.446  -0.091  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.479   1.068  -0.367  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.349   0.076  -0.978  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.648  -0.175  -2.286  0.00  0.00           C+0
HETATM   26  N   UNK     0       2.516  -1.205  -2.354  0.00  0.00           N+0
HETATM   27  C   UNK     0       2.805  -1.653  -1.108  0.00  0.00           C+0
HETATM   28  C   UNK     0       3.600  -2.644  -0.591  0.00  0.00           C+0
HETATM   29  C   UNK     0       3.672  -2.840   0.770  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.956  -2.057   1.651  0.00  0.00           C+0
HETATM   31 Cl   UNK     0       3.102  -2.369   3.361  0.00  0.00          Cl+0
HETATM   32  C   UNK     0       2.164  -1.068   1.117  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.090  -0.868  -0.255  0.00  0.00           C+0
HETATM   34  H   UNK     0       3.914   4.864  -1.510  0.00  0.00           H+0
HETATM   35  H   UNK     0       2.705   6.231  -1.777  0.00  0.00           H+0
HETATM   36  H   UNK     0       2.862   4.938  -2.986  0.00  0.00           H+0
HETATM   37  H   UNK     0      -0.415   4.073   0.318  0.00  0.00           H+0
HETATM   38  H   UNK     0      -3.951   1.648   3.905  0.00  0.00           H+0
HETATM   39  H   UNK     0      -4.973   0.695   2.705  0.00  0.00           H+0
HETATM   40  H   UNK     0      -4.769   2.454   2.552  0.00  0.00           H+0
HETATM   41  H   UNK     0      -1.046  -0.396   2.906  0.00  0.00           H+0
HETATM   42  H   UNK     0      -2.129  -2.777   2.763  0.00  0.00           H+0
HETATM   43  H   UNK     0      -3.022  -4.466   0.727  0.00  0.00           H+0
HETATM   44  H   UNK     0      -3.245  -4.612  -1.709  0.00  0.00           H+0
HETATM   45  H   UNK     0      -1.496  -0.690  -2.097  0.00  0.00           H+0
HETATM   46  H   UNK     0       1.238   0.385  -3.123  0.00  0.00           H+0
HETATM   47  H   UNK     0       2.925  -1.624  -3.213  0.00  0.00           H+0
HETATM   48  H   UNK     0       4.154  -3.249  -1.290  0.00  0.00           H+0
HETATM   49  H   UNK     0       4.299  -3.621   1.167  0.00  0.00           H+0
HETATM   50  H   UNK     0       1.603  -0.455   1.812  0.00  0.00           H+0
CONECT    1    2   34   35   36                                             
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   23                                                  
CONECT    6    5    7   37                                                  
CONECT    7    6    8   12                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   38   39   40                                             
CONECT   12    7   13   23                                                  
CONECT   13   12   14   22                                                  
CONECT   14   13   15   41                                                  
CONECT   15   14   16   42                                                  
CONECT   16   15   17   22                                                  
CONECT   17   16   18   43                                                  
CONECT   18   17   19   44                                                  
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   45                                                  
CONECT   22   21   13   16                                                  
CONECT   23   12   24    5                                                  
CONECT   24   23   25   33                                                  
CONECT   25   24   26   46                                                  
CONECT   26   25   27   47                                                  
CONECT   27   26   28   33                                                  
CONECT   28   27   29   48                                                  
CONECT   29   28   30   49                                                  
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   50                                                  
CONECT   33   32   24   27                                                  
CONECT   34    1                                                            
CONECT   35    1                                                            
CONECT   36    1                                                            
CONECT   37    6                                                            
CONECT   38   11                                                            
CONECT   39   11                                                            
CONECT   40   11                                                            
CONECT   41   14                                                            
CONECT   42   15                                                            
CONECT   43   17                                                            
CONECT   44   18                                                            
CONECT   45   21                                                            
CONECT   46   25                                                            
CONECT   47   26                                                            
CONECT   48   28                                                            
CONECT   49   29                                                            
CONECT   50   32                                                            
MASTER        0    0    0    0    0    0    0    0   50    0  108    0
END

RDKit          3D

50 54  0  0  0  0  0  0  0  0999 V2000
    2.9124    5.1487   -1.8951 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8822    4.4500   -1.2201 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7823    3.0683   -1.1916 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6655    2.4259   -1.8059 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6852    2.4362   -0.4691 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3126    3.0186    0.2203 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1342    2.0964    0.7498 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3258    2.3205    1.5598 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6514    3.5073    1.8105 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0913    1.2920    2.0494 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2484    1.5106    2.8361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6507    0.8354    0.3892 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2124   -0.4605    0.7315 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3531   -0.9511    2.0070 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9076   -2.1733    1.9615 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1385   -2.5051    0.6804 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6925   -3.6503    0.1144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8123   -3.7181   -1.2757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3810   -2.6590   -2.0150 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5112   -2.6952   -3.7801 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.8287   -1.5138   -1.4772 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7092   -1.4461   -0.0910 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4785    1.0678   -0.3668 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3494    0.0756   -0.9775 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6483   -0.1745   -2.2857 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5156   -1.2052   -2.3544 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8053   -1.6529   -1.1082 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5999   -2.6436   -0.5905 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6718   -2.8400    0.7701 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9564   -2.0572    1.6506 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1016   -2.3693    3.3612 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.1645   -1.0684    1.1166 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0902   -0.8683   -0.2546 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9135    4.8645   -1.5103 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7048    6.2311   -1.7772 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8620    4.9381   -2.9858 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4146    4.0729    0.3179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9510    1.6475    3.9054 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9729    0.6950    2.7049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7694    2.4538    2.5524 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0464   -0.3964    2.9062 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1290   -2.7765    2.7634 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0223   -4.4659    0.7269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2448   -4.6115   -1.7094 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4963   -0.6904   -2.0970 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2376    0.3851   -3.1230 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9246   -1.6243   -3.2130 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1540   -3.2492   -1.2899 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2989   -3.6211    1.1668 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6027   -0.4546    1.8118 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  1  0
  7 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 19 21  1  0
 21 22  2  0
 12 23  1  0
 23 24  1  0
 24 25  2  0
 25 26  1  0
 26 27  1  0
 27 28  2  0
 28 29  1  0
 29 30  2  0
 30 31  1  0
 30 32  1  0
 32 33  2  0
 23  5  2  0
 33 24  1  0
 22 13  1  0
 33 27  1  0
 22 16  1  0
  1 34  1  0
  1 35  1  0
  1 36  1  0
  6 37  1  0
 11 38  1  0
 11 39  1  0
 11 40  1  0
 14 41  1  0
 15 42  1  0
 17 43  1  0
 18 44  1  0
 21 45  1  0
 25 46  1  0
 26 47  1  0
 28 48  1  0
 29 49  1  0
 32 50  1  0
M  END

View in JSmol View NMR Assignments View DFT Assignments 3D Conformers

Synonyms

Value	Source
2,5-Dimethyl 3,4-bis(5-chloro-1H-indol-3-yl)-1H-pyrrole-2,5-dicarboxylic acid	Generator

Chemical Formula

C₂₄H₁₇Cl₂N₃O₄

Average Mass

482.3200 Da

Monoisotopic Mass

481.05961 Da

IUPAC Name

2,5-dimethyl 3,4-bis(5-chloro-1H-indol-3-yl)-1H-pyrrole-2,5-dicarboxylate

Traditional Name

lynamicin D

CAS Registry Number

Not Available

SMILES

COC(=O)C1=C(C2=CNC3=C2C=C(Cl)C=C3)C(=C(N1)C(=O)OC)C1=CNC2=C1C=C(Cl)C=C2

InChI Identifier

InChI=1S/C24H17Cl2N3O4/c1-32-23(30)21-19(15-9-27-17-5-3-11(25)7-13(15)17)20(22(29-21)24(31)33-2)16-10-28-18-6-4-12(26)8-14(16)18/h3-10,27-29H,1-2H3

InChI Key

YYBKJQDTRQASSS-UHFFFAOYSA-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
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 125 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 150 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 175 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 225 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 250 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, chcl3, 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
Actinomyces	NPAtlas	18842058
Marinispora sp.	-	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as indoles. Indoles are compounds containing an indole moiety, which consists of pyrrole ring fused to benzene to form 2,3-benzopyrrole.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indoles

Direct Parent

Indoles

Alternative Parents

Substituents

Indole
Pyrrole-2-carboxylic acid or derivatives
Aryl chloride
Aryl halide
Benzenoid
Substituted pyrrole
Heteroaromatic compound
Pyrrole
Methyl ester
Carboxylic acid ester
Carboxylic acid derivative
Azacycle
Organooxygen compound
Organonitrogen compound
Organochloride
Organohalogen compound
Organic nitrogen compound
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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	5.09	ALOGPS
logP	5.6	ChemAxon
logS	-6.1	ALOGPS
pKa (Strongest Acidic)	7.21	ChemAxon
pKa (Strongest Basic)	-6.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	99.97 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	126.68 m³·mol⁻¹	ChemAxon
Polarizability	47.99 Å³	ChemAxon
Number of Rings	5	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

NPA019793

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00048762

Chemspider ID

9504102

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11329151

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

McArthur KA, Mitchell SS, Tsueng G, Rheingold A, White DJ, Grodberg J, Lam KS, Potts BC: Lynamicins A-E, chlorinated bisindole pyrrole antibiotics from a novel marine actinomycete. J Nat Prod. 2008 Oct;71(10):1732-7. doi: 10.1021/np800286d. Epub 2008 Oct 9. [PubMed:18842058 ]

Showing NP-Card for Lynamicin D (NP0008032)

MOL for NP0008032 (Lynamicin D)

3D MOL for NP0008032 (Lynamicin D)

3D SDF for NP0008032 (Lynamicin D)

3D-SDF for NP0008032 (Lynamicin D)

PDB for NP0008032 (Lynamicin D)

3D PDB for NP0008032 (Lynamicin D)

SMILES for NP0008032 (Lynamicin D)

INCHI for NP0008032 (Lynamicin D)

Structure for NP0008032 (Lynamicin D)

3D Structure for NP0008032 (Lynamicin D)