Structure of PDB 5qay Chain D Binding Site BS01

Receptor Information

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

EWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFK
IPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVY
QEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFL
RKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWV
GWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP

Ligand information

• Ligand ID: X6P
• InChI: InChI=1S/C12H11NO2/c1-13-7-3-6-11(13)9-4-2-5-10(8-9)12(14)15/h2-8H,1H3,(H,14,15)
• InChIKey: UIRGFNLTEWMULM-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: Cn1cccc1c2cccc(c2)C(=O)O
  CACTVS 3.385: Cn1cccc1c2cccc(c2)C(O)=O
• Formula: C12 H11 N O2
• Name: 3-(1-methylpyrrol-2-yl)benzoic acid
• ChEMBL: CHEMBL4162292
• PDB chain: 5qay Chain D Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5qay A focused fragment library targeting the antibiotic resistance enzyme - Oxacillinase-48: Synthesis, structural evaluation and inhibitor design.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): I102 R250
• Binding residue (residue number reindexed from 1): I79 R227
• Annotation score: 1
• Binding affinity: MOAD: Kd=590uM

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
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0017001 antibiotic catabolic process
• GO:0046677 response to antibiotic
• GO:0071555 cell wall organization

External links

• PDB: RCSB:5qay, PDBe:5qay, PDBj:5qay
• PDBsum: 5qay
• PubMed: 29348071
• UniProt: Q6XEC0