Structure of PDB 5o7n Chain B Binding Site BS03

Receptor Information

>5o7n Chain B (length=232) Species: 573 (Klebsiella pneumoniae)

EYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELL
LIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGV
ATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHST
DNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYP
EAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRS

Ligand information

• Ligand ID: 9NK
• InChI: InChI=1S/C16H21NO3S/c18-15(17-9-5-4-8-14(17)16(19)20)13(11-21)10-12-6-2-1-3-7-12/h1-3,6-7,13-14,21H,4-5,8-11H2,(H,19,20)/t13-,14-/m1/s1
• InChIKey: BUVJKPXAJVVXFT-ZIAGYGMSSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: c1ccc(cc1)CC(CS)C(=O)N2CCCCC2C(=O)O
  OpenEye OEToolkits 2.0.6: c1ccc(cc1)C[C@H](CS)C(=O)N2CCCC[C@@H]2C(=O)O
  CACTVS 3.385: OC(=O)[C@H]1CCCCN1C(=O)[C@@H](CS)Cc2ccccc2
  CACTVS 3.385: OC(=O)[CH]1CCCCN1C(=O)[CH](CS)Cc2ccccc2
• Formula: C16 H21 N O3 S
• Name: (2~{R})-1-[(2~{S})-2-(phenylmethyl)-3-sulfanyl-propanoyl]piperidine-2-carboxylic acid
• PDB chain: 5o7n Chain B Residue 305

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5o7n Challenges in the Development of a Thiol-Based Broad-Spectrum Inhibitor for Metallo-beta-Lactamases.
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): Y67 H116 D118 H179 G209 N210 H240
• Binding residue (residue number reindexed from 1): Y36 H85 D87 H148 G178 N179 H209
• Annotation score: 1

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:5o7n, PDBe:5o7n, PDBj:5o7n
• PDBsum: 5o7n
• PubMed: 29172434
• UniProt: A0A173FE28