coumamycin   Click here for help

GtoPdb Ligand ID: 10879

Synonyms: coumermycin A1 | notomycin
PDB Ligand
Compound class: Synthetic organic
Comment: Coumamycin is an antibacterial compound, that inhibits bacterial topoisomerase activity [1,3], and which has activity against Gram-positive bacteria.

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2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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Hydrogen bond acceptors 14
Hydrogen bond donors 9
Rotatable bonds 18
Topological polar surface area 354.89
Molecular weight 1109.38
XLogP 7.06
No. Lipinski's rules broken 4

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

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Canonical SMILES CO[C@@H]1[C@@H](OC(=O)c2ccc([nH]2)C)[C@@H](O)[C@@H](OC1(C)C)Oc1ccc2c(c1C)oc(=O)c(c2O)NC(=O)c1c[nH]c(c1C)C(=O)Nc1c(=O)oc2c(c1O)ccc(c2C)O[C@@H]1OC(C)(C)[C@@H]([C@H]([C@H]1O)OC(=O)c1ccc([nH]1)C)OC
Isomeric SMILES CO[C@@H]1[C@@H](OC(=O)c2ccc([nH]2)C)[C@@H](O)[C@@H](OC1(C)C)Oc1ccc2c(c1C)oc(=O)c(c2O)NC(=O)c1c[nH]c(c1C)C(=O)Nc1c(=O)oc2c(c1O)ccc(c2C)O[C@@H]1OC(C)(C)[C@@H]([C@H]([C@H]1O)OC(=O)c1ccc([nH]1)C)OC
InChI InChI=1S/C55H59N5O20/c1-21-12-16-29(57-21)48(67)77-42-38(63)52(79-54(6,7)44(42)71-10)73-31-18-14-26-36(61)34(50(69)75-40(26)24(31)4)59-46(65)28-20-56-33(23(28)3)47(66)60-35-37(62)27-15-19-32(25(5)41(27)76-51(35)70)74-53-39(64)43(45(72-11)55(8,9)80-53)78-49(68)30-17-13-22(2)58-30/h12-20,38-39,42-45,52-53,56-58,61-64H,1-11H3,(H,59,65)(H,60,66)/t38-,39-,42+,43+,44-,45-,52-,53-/m1/s1
InChI Key WTIJXIZOODAMJT-DHFGXMAYSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
Classification Click here for help
Compound class Synthetic organic
IUPAC Name Click here for help
[(3R,4S,5R,6R)-5-hydroxy-6-[4-hydroxy-3-[[5-[[4-hydroxy-7-[(2R,3R,4S,5R)-3-hydroxy-5-methoxy-6,6-dimethyl-4-(5-methyl-1H-pyrrole-2-carbonyl)oxyoxan-2-yl]oxy-8-methyl-2-oxochromen-3-yl]carbamoyl]-4-methyl-1H-pyrrole-3-carbonyl]amino]-8-methyl-2-oxochromen-7-yl]oxy-3-methoxy-2,2-dimethyloxan-4-yl] 5-methyl-1H-pyrrole-2-carboxylate
International Nonproprietary Names Click here for help
INN number INN
1948 coumamycin
Synonyms Click here for help
coumermycin A1 | notomycin
Database Links Click here for help
Specialist databases
Antibiotic DB Antibiotic DB Database logo Coumermycin A1
Other databases
CAS Registry No. 4434-05-3 (source: WHO INN record)
GtoPdb PubChem SID 405560320
PubChem CID 54675768
RCSB PDB Ligand BHW
Search Google for chemical match using the InChIKey WTIJXIZOODAMJT-DHFGXMAYSA-N
Search Google for chemicals with the same backbone WTIJXIZOODAMJT
Search PubMed clinical trials coumamycin
Search PubMed titles coumamycin
Search PubMed titles/abstracts coumamycin
UniChem Compound Search for chemical match using the InChIKey WTIJXIZOODAMJT-DHFGXMAYSA-N
UniChem Connectivity Search for chemical match using the InChIKey WTIJXIZOODAMJT-DHFGXMAYSA-N

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MedChemExpress
Coumermycin A1 (links to external site)
Cat. No. HY-N7452