pyridomycin   Click here for help

GtoPdb Ligand ID: 13449

Synonyms: erizomycin
PDB Ligand
Compound class: Natural product
Comment: Pyridomycin is a natural product with potent antimycobacterial activity, produced by the Actinobacteria Streptomyces pyridomyceticus and Dactylosporangium fulvum, and which was first reported in 1953 [3]. It is an inhibitor of Mycobacterium enoyl acyl carrier protein reductase (InhA) [2], a clinically validated target and key enzyme involved in the synthesis of mycolic acid, an essential component of the mycobacterial cell wall.
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 12
Hydrogen bond donors 4
Rotatable bonds 6
Topological polar surface area 175.98
Molecular weight 540.57
XLogP 0.73
No. Lipinski's rules broken 2

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 CC/C(=C\1/C(=O)O[C@H](C)[C@@H](C(=O)N[C@@H](CC2=CC=CN=C2)[C@H]([C@@H](C)C(=O)O1)O)NC(=O)C3=NC=CC=C3O)/C
Isomeric SMILES CC/C(=C\1/C(=O)O[C@@H]([C@@H](C(=O)N[C@H]([C@H]([C@H](C(=O)O1)C)O)CC2=CN=CC=C2)NC(=O)C3=C(C=CC=N3)O)C)/C
InChI InChI=1S/C27H32N4O8/c1-5-14(2)23-27(37)38-16(4)20(31-25(35)21-19(32)9-7-11-29-21)24(34)30-18(12-17-8-6-10-28-13-17)22(33)15(3)26(36)39-23/h6-11,13,15-16,18,20,22,32-33H,5,12H2,1-4H3,(H,30,34)(H,31,35)/b23-14-/t15-,16-,18+,20+,22+/m1/s1
InChI Key WHIKSLGSXKIHCA-IGCCMALHSA-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/)
No information available.
Mechanism Of Action and Pharmacodynamic Effects Click here for help
Pyridomycin reduces mycolic acid synthesis in M. tuberculosis, by inhibiting InhA directly as a competitive inhibitor of the NADH‐binding site [2]. In a further study, the co-crystal structure revealed that pyridomycin blocks both the NADH cofactor- and lipid substrate-binding pockets of InhA [1].