Structure of PDB 6q5b Chain A Binding Site BS01

Receptor Information

>6q5b Chain A (length=233) Species: 573 (Klebsiella pneumoniae)

EWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLAASTFK
IPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVY
QEFARQIGEARMSKMLHAFDYGNEDIDGGIRISATEQISFLRKLYHNKLH
VSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNV
WFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP

Ligand information

• Ligand ID: NXL
• InChI: InChI=1S/C7H13N3O6S/c8-7(12)6-2-1-5(3-10(6)4-11)9-16-17(13,14)15/h4-6,9H,1-3H2,(H2,8,12)(H,13,14,15)/t5-,6+/m1/s1
• InChIKey: WJDGWXPPFHLLNL-RITPCOANSA-N
• SMILES:
  ACDLabs 12.01: O=CN1C(C(N)=O)CCC(C1)NOS(=O)(O)=O
  OpenEye OEToolkits 1.7.6: C1CC(N(CC1NOS(=O)(=O)O)C=O)C(=O)N
  CACTVS 3.385: NC(=O)[CH]1CC[CH](CN1C=O)NO[S](O)(=O)=O
  OpenEye OEToolkits 1.7.6: C1C[C@H](N(C[C@@H]1NOS(=O)(=O)O)C=O)C(=O)N
  CACTVS 3.385: NC(=O)[C@@H]1CC[C@H](CN1C=O)NO[S](O)(=O)=O
• Formula: C7 H13 N3 O6 S
• Name: (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide;
  avibactam, bound form;
  NXL104, bound form
• ZINC: ZINC000098209247
• PDB chain: 6q5b Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6q5b OXA-48-Mediated Ceftazidime-Avibactam Resistance Is Associated with Evolutionary Trade-Offs.
• Resolution: 2.22 Å
• Binding residue (original residue number in PDB): A69 S70 S118 T209 G210 Y211 R250
• Binding residue (residue number reindexed from 1): A46 S47 S95 T177 G178 Y179 R218
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=5.89,IC50=1.3uM

Enzymatic activity

• Catalytic site (original residue number in PDB): S70 K73 S118 Y123 Y211
• Catalytic site (residue number reindexed from 1): S47 K50 S95 Y100 Y179
• 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:6q5b, PDBe:6q5b, PDBj:6q5b
• PDBsum: 6q5b
• PubMed: 30918055
• UniProt: Q6XEC0