Structure of PDB 8vbv Chain B Binding Site BS01

Receptor Information

>8vbv Chain B (length=504) Species: 2043664 (Staphylococcaceae bacterium)

QQPERGKIYDRNGKVLAEDVERYKLVAVIDKKASANSKKPRHVVDKKETA
KKLSTVIDMKPEEIEKRLSQKKAFQIEFGRKGTNLTYQDKLKIEKMNLPG
ISLLPETERFYPNGNFASHLIGRAQKNPDTGELKGALGVEKIFDSYLSGK
RGDDVHLTIDSNIQVFVEEALDGMVERYQPKDLFAVVMDAKTGEILAYSQ
RPTFNPETGKDFGKKWANDLYQNTYEPGSTFKSYGLAAAIQEGAFDPDKK
YKSGHRDIMGSRISDWNRVGWGEIPMSLGFTYSSNTLMMHLQDLVGADKM
KSWYERFGFGKSTKGMFDGEAPGQIGWSNELQQKTSSFGQSTTVTPVQML
QAQSAFFNDGNMLKPWFVNSVENPVSKRQFYKGQKQIAGKPITKDTAEKV
EKQLDLVVNSKKSHAANYRIDGYEVEGKTGTAQVAAPNGGGYVKGPNPYF
VSFMGDAPKKNPKVIVYAGMSLAQKNDQEAYELGVSKAFKPIMENTLKYL
NVGK

Ligand information

• Ligand ID: 63U
• InChI: InChI=1S/C16H19N3O4S/c1-9-8-24-15(19-13(9)16(22)23)11(7-20)18-14(21)12(17)10-5-3-2-4-6-10/h2-7,11-12,15,19H,8,17H2,1H3,(H,18,21)(H,22,23)/t11-,12-,15+/m1/s1
• InChIKey: YUNPQAOWKVWRNR-JMSVASOKSA-N
• SMILES:
  ACDLabs 12.01: O=C(C1=C(C)CSC(N1)C(C=O)NC(C(c2ccccc2)N)=O)O
  OpenEye OEToolkits 2.0.4: CC1=C(NC(SC1)C(C=O)NC(=O)C(c2ccccc2)N)C(=O)O
  OpenEye OEToolkits 2.0.4: CC1=C(N[C@@H](SC1)[C@@H](C=O)NC(=O)[C@@H](c2ccccc2)N)C(=O)O
  CACTVS 3.385: CC1=C(N[CH](SC1)[CH](NC(=O)[CH](N)c2ccccc2)C=O)C(O)=O
  CACTVS 3.385: CC1=C(N[C@@H](SC1)[C@H](NC(=O)[C@H](N)c2ccccc2)C=O)C(O)=O
• Formula: C16 H19 N3 O4 S
• Name: (2S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
• ZINC: ZINC000584905337
• PDB chain: 8vbv Chain B Residue 801

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8vbv Structural and kinetic analysis of the monofunctional Staphylococcus aureus PBP1.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): S314 W351 S368 T514 T516 Y534
• Binding residue (residue number reindexed from 1): S229 W266 S283 T429 T431 Y449
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0008658 penicillin binding

External links

• PDB: RCSB:8vbv, PDBe:8vbv, PDBj:8vbv
• PDBsum: 8vbv
• PubMed: 38527711
• UniProt: Q2FZ94