Structure of PDB 5k48 Chain A Binding Site BS01

Receptor Information

>5k48 Chain A (length=231) Species: 287 (Pseudomonas aeruginosa)

EYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELL
LIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGV
ATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHST
DNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYP
EAQFVIPGHGLPGGLDLLKHTTNVVKAHTNR

Ligand information

• Ligand ID: S5Z
• InChI: InChI=1S/C14H12O2S/c15-14(16)13-7-6-11(8-12(13)9-17)10-4-2-1-3-5-10/h1-8,17H,9H2,(H,15,16)
• InChIKey: OJGNJYVRHUYKQS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: OC(=O)c1ccc(cc1CS)c2ccccc2
  OpenEye OEToolkits 2.0.5: c1ccc(cc1)c2ccc(c(c2)CS)C(=O)O
• Formula: C14 H12 O2 S
• Name: 4-phenyl-2-(sulfanylmethyl)benzoic acid
• ChEMBL: CHEMBL4076158
• PDB chain: 5k48 Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5k48 In Silico Fragment-Based Design Identifies Subfamily B1 Metallo-beta-lactamase Inhibitors.
• Resolution: 1.744 Å
• Binding residue (original residue number in PDB): Y67 D118 H179 N210 H240
• Binding residue (residue number reindexed from 1): Y36 D87 H148 N179 H209
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=6.60,Kd=0.251uM

Enzymatic activity

• Catalytic site (original residue number in PDB): H114 H116 D118 H179 C198 Y201 N210 H240
• Catalytic site (residue number reindexed from 1): H83 H85 D87 H148 C167 Y170 N179 H209
• Enzyme Commision number: 3.5.2.6: beta-lactamase.

Gene Ontology

Molecular Function

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

Biological Process

• GO:0017001 antibiotic catabolic process

External links

• PDB: RCSB:5k48, PDBe:5k48, PDBj:5k48
• PDBsum: 5k48
• PubMed: 29271657
• UniProt: Q9K2N0