MiMeDB: Showing metabocard for Lynamicin C (MMDBc0002090)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-14 20:37:49 UTC

Update Date

2022-08-31 06:18:57 UTC

Metabolite ID

MMDBc0002090

Metabolite Identification

Common Name

Lynamicin C

Description

CHEMBL523274 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. CHEMBL523274 is a very weakly acidic compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004161502142D          

 27 31  0  0  0  0            999 V2000
    5.1323    2.5204    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    4.4179    2.1079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7034    2.5204    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9889    2.1079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2043    2.3628    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7194    1.6954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2043    1.0280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9494    0.2433    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4343   -0.4241    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9494   -1.0915    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1647   -0.8366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1647   -0.0116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4973    0.4733    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2873    0.2184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7722    0.8858    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2873    1.5533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4588    2.3602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1543    2.9123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0173    3.7192    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.9389    2.6573    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5520    3.2094    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.1104    1.8504    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4973    1.2983    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9889    1.2829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7034    0.8704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4179    1.2829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1323    0.8704    0.0000 Cl  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
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
  8 12  1  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  1  0  0  0  0
 18 20  2  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  2  0  0  0  0
 13 23  1  0  0  0  0
 16 23  1  0  0  0  0
  7 24  1  0  0  0  0
  4 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
  2 26  2  0  0  0  0
 26 27  1  0  0  0  0
M  END


  Mrv1533004161502142D          

 27 31  0  0  0  0            999 V2000
    5.1323    2.5204    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    4.4179    2.1079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7034    2.5204    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9889    2.1079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2043    2.3628    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7194    1.6954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2043    1.0280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9494    0.2433    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4343   -0.4241    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9494   -1.0915    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1647   -0.8366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1647   -0.0116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4973    0.4733    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2873    0.2184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7722    0.8858    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2873    1.5533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4588    2.3602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1543    2.9123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0173    3.7192    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.9389    2.6573    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5520    3.2094    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.1104    1.8504    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4973    1.2983    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9889    1.2829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7034    0.8704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4179    1.2829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1323    0.8704    0.0000 Cl  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
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
  8 12  1  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  1  0  0  0  0
 18 20  2  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  2  0  0  0  0
 13 23  1  0  0  0  0
 16 23  1  0  0  0  0
  7 24  1  0  0  0  0
  4 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
  2 26  2  0  0  0  0
 26 27  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0002090

> <DATABASE_NAME>
MIME

> <SMILES>
ClC1=C(Cl)C=C2C(NC=C2C2=CNC=C2C2=CNC3=CC(Cl)=C(Cl)C=C23)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C20H11Cl4N3/c21-15-1-9-13(7-26-19(9)3-17(15)23)11-5-25-6-12(11)14-8-27-20-4-18(24)16(22)2-10(14)20/h1-8,25-27H

> <INCHI_KEY>
BMSRAYDJPZCVMP-UHFFFAOYSA-N

> <FORMULA>
C20H11Cl4N3

> <MOLECULAR_WEIGHT>
435.13

> <EXACT_MASS>
432.9707082

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
41.040757415022966

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5,6-dichloro-3-[4-(5,6-dichloro-1H-indol-3-yl)-1H-pyrrol-3-yl]-1H-indole

> <ALOGPS_LOGP>
6.55

> <JCHEM_LOGP>
6.961283343999999

> <ALOGPS_LOGS>
-6.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.598781539545016

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.990868492857242

> <JCHEM_POLAR_SURFACE_AREA>
47.37

> <JCHEM_REFRACTIVITY>
112.48139999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.21e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
lynamicin C

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1 Cl   UNK     0       9.580   4.705   0.000  0.00  0.00          Cl+0
HETATM    2  C   UNK     0       8.247   3.935   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.913   4.705   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.579   3.935   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       4.115   4.411   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       3.210   3.165   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.115   1.919   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.639   0.454   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.544  -0.792   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       3.639  -2.038   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       2.174  -1.562   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.174  -0.022   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.928   0.884   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.536   0.408   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      -1.442   1.654   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0      -0.536   2.899   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.857   4.406   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.288   5.436   0.000  0.00  0.00           C+0
HETATM   19 Cl   UNK     0      -0.032   6.943   0.000  0.00  0.00          Cl+0
HETATM   20  C   UNK     0       1.753   4.960   0.000  0.00  0.00           C+0
HETATM   21 Cl   UNK     0       2.897   5.991   0.000  0.00  0.00          Cl+0
HETATM   22  C   UNK     0       2.073   3.454   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.928   2.424   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.579   2.395   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.913   1.625   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.247   2.395   0.000  0.00  0.00           C+0
HETATM   27 Cl   UNK     0       9.580   1.625   0.000  0.00  0.00          Cl+0
CONECT    1    2                                                            
CONECT    2    1    3   26                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   24                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   24                                                  
CONECT    8    7    9   12                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    8   13                                                  
CONECT   13   12   14   23                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   23                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   13   16                                                  
CONECT   24    7    4   25                                                  
CONECT   25   24   26                                                       
CONECT   26   25    2   27                                                  
CONECT   27   26                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   62    0
END

Synonyms

Not Available

Molecular Formula

C₂₀H₁₁Cl₄N₃

Average Mass

435.13

Monoisotopic Mass

432.9707082

IUPAC Name

5,6-dichloro-3-[4-(5,6-dichloro-1H-indol-3-yl)-1H-pyrrol-3-yl]-1H-indole

Traditional Name

lynamicin C

CAS Registry Number

Not Available

SMILES

ClC1=C(Cl)C=C2C(NC=C2C2=CNC=C2C2=CNC3=CC(Cl)=C(Cl)C=C23)=C1

InChI Identifier

InChI=1S/C20H11Cl4N3/c21-15-1-9-13(7-26-19(9)3-17(15)23)11-5-25-6-12(11)14-8-27-20-4-18(24)16(22)2-10(14)20/h1-8,25-27H

InChI Key

BMSRAYDJPZCVMP-UHFFFAOYSA-N

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
Benzenoid
Substituted pyrrole
Aryl halide
Aryl chloride
Heteroaromatic compound
Pyrrole
Azacycle
Organic nitrogen compound
Hydrocarbon derivative
Organonitrogen compound
Organochloride
Organohalogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.00022 g/L	ALOGPS
logP	6.55	ALOGPS
logP	6.96	ChemAxon
logS	-6.3	ALOGPS
pKa (Strongest Acidic)	14.99	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	47.37 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	112.48 m³·mol⁻¹	ChemAxon
Polarizability	41.04 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

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Not Available

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Actinobacteria	1	Human ; Human feces; Human saliva; Human urine; Human supragingival plaque; Human sputum; Human subgingival plaque	Metabolic reconstruction

Exposure Sources

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11385005

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Lynamicin C (MMDBc0002090)

MOL for #<Metabolite:0x00007fdb44013548>

3D MOL for #<Metabolite:0x00007fdb44013548>

3D SDF for #<Metabolite:0x00007fdb44013548>

3D-SDF for #<Metabolite:0x00007fdb44013548>

PDB for #<Metabolite:0x00007fdb44013548>

3D PDB for #<Metabolite:0x00007fdb44013548>

SMILES for #<Metabolite:0x00007fdb44013548>

INCHI for #<Metabolite:0x00007fdb44013548>

Structure for #<Metabolite:0x00007fdb44013548>

3D Structure for #<Metabolite:0x00007fdb44013548>