Structure of PDB 6mkq Chain A Binding Site BS01

Receptor Information
>6mkq Chain A (length=262) Species: 666 (Vibrio cholerae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NKNMADIEAAFEGRVGVYAINTGSGKAYSYRANERFPLCSSFKAFLAAAV
LKMDQDSPGVLLEKVNYHNRTMEPHSPITEKFQSQGMAVGELAAATLQYS
DNGAANLLMEKYIKGPEGMTQFMNSIGDTKFRLDRWELDLNSAIPGDERD
TSTPKAVAESLNKLISNTVLDNYHQEIFKKWMIGNTTGDNRIRAAVPDGW
VVGDKTGTCGKYGTANDHAFILQGNNAAPLILSIYTTRKGEHMKHDDEVI
AKAARIAIENVK
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 chain6mkq Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6mkq Molecular Basis for the Potent Inhibition of the Emerging Carbapenemase VCC-1 by Avibactam.
Resolution1.9 Å
Binding residue
(original residue number in PDB)
C42 S43 S103 T190 T209 G210 T211
Binding residue
(residue number reindexed from 1)
C39 S40 S100 T187 T206 G207 T208
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.16,Kd=0.686uM
Enzymatic activity
Catalytic site (original residue number in PDB) S43 K46 S103 E140 K208 T211
Catalytic site (residue number reindexed from 1) S40 K43 S100 E137 K205 T208
Enzyme Commision number 3.5.2.6: beta-lactamase.
Gene Ontology
Molecular Function
GO:0008800 beta-lactamase activity
Biological Process
GO:0017001 antibiotic catabolic process
GO:0030655 beta-lactam antibiotic catabolic process
GO:0046677 response to antibiotic

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:6mkq, PDBe:6mkq, PDBj:6mkq
PDBsum6mkq
PubMed30782990
UniProtA0A0U3IB62

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