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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Physico-chemical Properties
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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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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