Structure of PDB 5dva Chain D Binding Site BS01

Receptor Information

>5dva Chain D (length=242) Species: 573 (Klebsiella pneumoniae)

EWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFK
IPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVY
QEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFL
RKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWV
GWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP

Ligand information

• Ligand ID: 5FL
• InChI: InChI=1S/C12H9NO2/c14-12(15)11-3-1-2-10(8-11)9-4-6-13-7-5-9/h1-8H,(H,14,15)
• InChIKey: IYGIZNZSONLPSI-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: c2c(c1cccc(c1)C(=O)O)ccnc2
  OpenEye OEToolkits 1.9.2: c1cc(cc(c1)C(=O)O)c2ccncc2
  CACTVS 3.385: OC(=O)c1cccc(c1)c2ccncc2
• Formula: C12 H9 N O2
• Name: 3-(pyridin-4-yl)benzoic acid
• ChEMBL: CHEMBL3913021
• ZINC: ZINC000002563822
• PDB chain: 5dva Chain D Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dva Screening and Design of Inhibitor Scaffolds for the Antibiotic Resistance Oxacillinase-48 (OXA-48) through Surface Plasmon Resonance Screening.
• Resolution: 2.50004 Å
• Binding residue (original residue number in PDB): S118 Y211 S244 R250
• Binding residue (residue number reindexed from 1): S95 Y188 S221 R227
• Annotation score: 1
• Binding affinity: MOAD: Kd=280uM
  BindingDB: Kd=280000nM,IC50=250000nM

Enzymatic activity

• Catalytic site (original residue number in PDB): S70 K73 S118 Y123 W157 Y211
• Catalytic site (residue number reindexed from 1): S47 K50 S95 Y100 W134 Y188
• Enzyme Commision number: 3.5.2.6: beta-lactamase.

Gene Ontology

Molecular Function

• GO:0008658 penicillin binding
• GO:0008800 beta-lactamase activity

Biological Process

• GO:0017001 antibiotic catabolic process

External links

• PDB: RCSB:5dva, PDBe:5dva, PDBj:5dva
• PDBsum: 5dva
• PubMed: 27165692
• UniProt: Q6XEC0