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capuramycin   Click here for help

GtoPdb Ligand ID: 13471

Synonyms: A-500359 B | antibiotic 446-S3-1
PDB Ligand
Compound class: Natural product
Comment: Capuramycin is a nucleoside antibacterial compound, with activity against Gram-positive bacteria and mycobacteria, and that was initially isolated from the culture filtrate of Streptomyces griseus 446-S3 [5]. It inhibits phospho-N-acetylmuramoyl-pentapeptide-transferase (MraY, translocase I) [3], an essential enzyme in bacterial peptidoglycan biosynthesis.
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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Click here for structure editor
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 17
Hydrogen bond donors 7
Rotatable bonds 9
Topological polar surface area 248.31
Molecular weight 569.52
XLogP -3.48
No. Lipinski's rules broken 3

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]([C@H](N2C=CC(=O)NC2=O)O[C@@H]1[C@H](C(=O)N)O[C@@H]3[C@H]([C@H](C=C(C(=O)N[C@H]4CCCCNC4=O)O3)O)O)O
Isomeric SMILES CO[C@H]1[C@H]([C@@H](O[C@@H]1[C@H](C(=O)N)O[C@@H]2[C@H]([C@H](C=C(O2)C(=O)N[C@H]3CCCCNC3=O)O)O)N4C=CC(=O)NC4=O)O
InChI InChI=1S/C23H31N5O12/c1-37-15-14(32)21(28-7-5-12(30)27-23(28)36)39-16(15)17(18(24)33)40-22-13(31)10(29)8-11(38-22)20(35)26-9-4-2-3-6-25-19(9)34/h5,7-10,13-17,21-22,29,31-32H,2-4,6H2,1H3,(H2,24,33)(H,25,34)(H,26,35)(H,27,30,36)/t9-,10-,13-,14+,15-,16-,17+,21+,22+/m0/s1
InChI Key BISOEENGZHMDEO-RLXIHFJVSA-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 Natural product
IUPAC Name Click here for help
(4S,5S,6S)-6-[(1R)-2-amino-1-[(2S,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-4-hydroxy-3-methoxyoxolan-2-yl]-2-oxoethoxy]-4,5-dihydroxy-N-[(3S)-2-oxoazepan-3-yl]-5,6-dihydro-4H-pyran-2-carboxamide
Synonyms Click here for help
A-500359 B | antibiotic 446-S3-1
Database Links Click here for help
Specialist databases
Antibiotic DB Antibiotic DB Database logo Capuramycin
Other databases
BindingDB Ligand 50135599
CAS Registry No. 102770-00-3 (source: Scifinder)
ChEBI CHEBI:221360
ChEMBL Ligand CHEMBL96695
GtoPdb PubChem SID 500839881
PubChem CID 5487121
RCSB PDB Ligand NKM
Search Google for chemical match using the InChIKey BISOEENGZHMDEO-RLXIHFJVSA-N
Search Google for chemicals with the same backbone BISOEENGZHMDEO
UniChem Compound Search for chemical match using the InChIKey BISOEENGZHMDEO-RLXIHFJVSA-N
UniChem Connectivity Search for chemical match using the InChIKey BISOEENGZHMDEO-RLXIHFJVSA-N