Structure of PDB 4wmc Chain D Binding Site BS01

Receptor Information
>4wmc Chain D (length=236) Species: 573 (Klebsiella pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFK
IPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVY
QEFARQIGEARMSKMLHAFDYGNEDIFWLDGGIRISATEQISFLRKLYHN
KLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELD
DNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP
Ligand information
Ligand IDNXL
InChIInChI=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
InChIKeyWJDGWXPPFHLLNL-RITPCOANSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=CN1C(C(N)=O)CCC(C1)NOS(=O)(O)=O
OpenEye OEToolkits 1.7.6C1CC(N(CC1NOS(=O)(=O)O)C=O)C(=O)N
CACTVS 3.385NC(=O)[CH]1CC[CH](CN1C=O)NO[S](O)(=O)=O
OpenEye OEToolkits 1.7.6C1C[C@H](N(C[C@@H]1NOS(=O)(=O)O)C=O)C(=O)N
CACTVS 3.385NC(=O)[C@@H]1CC[C@H](CN1C=O)NO[S](O)(=O)=O
FormulaC7 H13 N3 O6 S
Name(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide;
avibactam, bound form;
NXL104, bound form
ChEMBL
DrugBank
ZINCZINC000098209247
PDB chain4wmc Chain D Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4wmc Molecular Basis of Selective Inhibition and Slow Reversibility of Avibactam against Class D Carbapenemases: A Structure-Guided Study of OXA-24 and OXA-48.
Resolution2.3 Å
Binding residue
(original residue number in PDB)
S70 S118 V120 T209 G210 Y211 R250
Binding residue
(residue number reindexed from 1)
S47 S95 V97 T180 G181 Y182 R221
Annotation score1
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 W128 Y182
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

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:4wmc, PDBe:4wmc, PDBj:4wmc
PDBsum4wmc
PubMed25406838
UniProtQ6XEC0

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