MiMeDB: Showing metabocard for Lynamicin B (MMDBc0006436)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-14 23:38:46 UTC

Update Date

2025-10-07 16:05:09 UTC

Metabolite ID

MMDBc0006436

Metabolite Identification

Common Name

Lynamicin B

Description

Lynamicin B is a chitinase inhibitor belonging to the class of natural metabolites. This compound has garnered attention for its potential use as a pesticide, specifically targeting lepidopteran pests by selectively inhibiting the chitinase enzyme OfChi-h from Ostrinia furnacalis, which is crucial for their growth and development (PMID:34797675 ). The crystal structure analysis of Lynamicin B bound to OfChi-h revealed a unique binding interaction, where the dichloroindolyl group occupies an unexplored pocket in the substrate-binding cleft, contributing to its specificity and competitive inhibition with a Ki value of 8.76 μM (PMID:34797675 ). Notably, Lynamicin B demonstrated high insecticidal activity against other lepidopteran species, including Mythimna separata and Spodoptera frugiperda, while showing no significant impact on Trichogramma ostriniae, a beneficial parasitoid (PMID:34797675 ). These findings suggest that Lynamicin B could be a valuable tool in pest management strategies, leveraging its selective action against target pests while minimizing effects on non-target species (PMID:37038745 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004241505182D          

 30 34  0  0  0  0            999 V2000
    3.4312   -3.5319    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6062   -3.5319    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1937   -2.8174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6062   -2.1030    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3687   -2.8174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -3.4849    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -3.2299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -2.4049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -1.9200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3529   -2.1750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8378   -1.5075    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3529   -0.8401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5244   -0.0331    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9113    0.5189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0829    1.3259    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.1267    0.2640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4864    0.8160    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.0448   -0.5430    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -1.0950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668   -1.5229    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   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  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 18 19  2  0  0  0  0
  9 19  1  0  0  0  0
 12 19  1  0  0  0  0
  8 20  1  0  0  0  0
  5 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 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  2  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 29 30  2  0  0  0  0
 21 30  1  0  0  0  0
 24 30  1  0  0  0  0
M  END


  Mrv1533004241505182D          

 30 34  0  0  0  0            999 V2000
    3.4312   -3.5319    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6062   -3.5319    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1937   -2.8174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6062   -2.1030    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3687   -2.8174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -3.4849    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -3.2299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -2.4049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -1.9200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3529   -2.1750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8378   -1.5075    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3529   -0.8401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5244   -0.0331    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9113    0.5189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0829    1.3259    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.1267    0.2640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4864    0.8160    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.0448   -0.5430    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -1.0950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668   -1.5229    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   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  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 18 19  2  0  0  0  0
  9 19  1  0  0  0  0
 12 19  1  0  0  0  0
  8 20  1  0  0  0  0
  5 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 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  2  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 29 30  2  0  0  0  0
 21 30  1  0  0  0  0
 24 30  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0006436

> <DATABASE_NAME>
MIME

> <SMILES>
COC(=O)C1=C(C(=CN1)C1=CNC2=CC(Cl)=C(Cl)C=C12)C1=CNC2=CC=C(Cl)C=C12

> <INCHI_IDENTIFIER>
InChI=1S/C22H14Cl3N3O2/c1-30-22(29)21-20(14-8-26-18-3-2-10(23)4-11(14)18)15(9-28-21)13-7-27-19-6-17(25)16(24)5-12(13)19/h2-9,26-28H,1H3

> <INCHI_KEY>
HJXJUNZGSRTQEN-UHFFFAOYSA-N

> <FORMULA>
C22H14Cl3N3O2

> <MOLECULAR_WEIGHT>
458.72

> <EXACT_MASS>
457.0151598

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
44

> <JCHEM_AVERAGE_POLARIZABILITY>
44.09040727481354

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl 3-(5-chloro-1H-indol-3-yl)-4-(5,6-dichloro-1H-indol-3-yl)-1H-pyrrole-2-carboxylate

> <ALOGPS_LOGP>
5.87

> <JCHEM_LOGP>
6.280716755333333

> <ALOGPS_LOGS>
-6.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.2146962729237

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.65264039864209

> <JCHEM_PKA_STRONGEST_BASIC>
-7.128669359018623

> <JCHEM_POLAR_SURFACE_AREA>
73.67

> <JCHEM_REFRACTIVITY>
119.57939999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.30e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
lynamicin B

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0       6.405  -6.593   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       4.865  -6.593   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       4.095  -5.259   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       4.865  -3.926   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.555  -5.259   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       1.650  -6.505   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       0.185  -6.029   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.185  -4.489   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.061  -3.584   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.525  -4.060   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      -3.431  -2.814   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0      -2.525  -1.568   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.846  -0.062   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.701   0.969   0.000  0.00  0.00           C+0
HETATM   15 Cl   UNK     0      -2.021   2.475   0.000  0.00  0.00          Cl+0
HETATM   16  C   UNK     0      -0.237   0.493   0.000  0.00  0.00           C+0
HETATM   17 Cl   UNK     0       0.908   1.523   0.000  0.00  0.00          Cl+0
HETATM   18  C   UNK     0       0.084  -1.014   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.061  -2.044   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM   23  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   28 Cl   UNK     0       7.591  -2.843   0.000  0.00  0.00          Cl+0
HETATM   29  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   20                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   20                                                  
CONECT    9    8   10   19                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   19                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18    9   12                                                  
CONECT   20    8    5   21                                                  
CONECT   21   20   22   30                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   30                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29   21   24                                                  
MASTER        0    0    0    0    0    0    0    0   30    0   68    0
END

Synonyms

Value	Source
Methyl 3-(5-chloro-1H-indol-3-yl)-4-(5,6-dichloro-1H-indol-3-yl)-1H-pyrrole-2-carboxylic acid	Generator

Molecular Formula

C₂₂H₁₄Cl₃N₃O₂

Average Mass

458.72

Monoisotopic Mass

457.0151598

IUPAC Name

methyl 3-(5-chloro-1H-indol-3-yl)-4-(5,6-dichloro-1H-indol-3-yl)-1H-pyrrole-2-carboxylate

Traditional Name

lynamicin B

CAS Registry Number

Not Available

SMILES

COC(=O)C1=C(C(=CN1)C1=CNC2=CC(Cl)=C(Cl)C=C12)C1=CNC2=CC=C(Cl)C=C12

InChI Identifier

InChI=1S/C22H14Cl3N3O2/c1-30-22(29)21-20(14-8-26-18-3-2-10(23)4-11(14)18)15(9-28-21)13-7-27-19-6-17(25)16(24)5-12(13)19/h2-9,26-28H,1H3

InChI Key

HJXJUNZGSRTQEN-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
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

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.00043 g/L	ALOGPS
logP	5.87	ALOGPS
logP	6.28	ChemAxon
logS	-6	ALOGPS
pKa (Strongest Acidic)	11.65	ChemAxon
pKa (Strongest Basic)	-7.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	73.67 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	119.58 m³·mol⁻¹	ChemAxon
Polarizability	44.09 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

Microbial Pathways

Pathways

This table shows at most 5 pathways. For the full list of associated pathways:

See All Associated Bacterial Pathways

Name	SMPDB/PathBank	Species

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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

Other Exposures

Source Type	Data Source	Reference

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

11271102

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 B (MMDBc0006436)

MOL for #<Metabolite:0x00007fb4d6d5df58>

3D MOL for #<Metabolite:0x00007fb4d6d5df58>

3D SDF for #<Metabolite:0x00007fb4d6d5df58>

3D-SDF for #<Metabolite:0x00007fb4d6d5df58>

PDB for #<Metabolite:0x00007fb4d6d5df58>

3D PDB for #<Metabolite:0x00007fb4d6d5df58>

SMILES for #<Metabolite:0x00007fb4d6d5df58>

INCHI for #<Metabolite:0x00007fb4d6d5df58>

Structure for #<Metabolite:0x00007fb4d6d5df58>

3D Structure for #<Metabolite:0x00007fb4d6d5df58>