Structure of PDB 6d3g Chain A Binding Site BS01

Receptor Information
>6d3g Chain A (length=279) Species: 546 (Citrobacter freundii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAQSPLLKEQIETIVTGKKATVGVAVWGPDDLEPLLLNPFEKFPMQSVFK
LHLAMLVLHQVDQGKLDLNQSVTVNRAAVLQNTWSPMMKDHQGDEFTVAV
QQLLQYSVSHSDNVACDLLFELVGGPQALHAYIQSLGVKEAAVVANEAQM
HADDQVQYQNWTSMKAAAQVLQKFEQKKQLSETSQALLWKWMVETTTGPQ
RLKGLLPAGTIVAHKTGTSGVRAGKTAATNDAGVIMLPDGRPLLVAVFVK
DSAESERTNEAIIAQVAQAAYQFELKKLS
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 chain6d3g Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6d3g Structural Insights into the Inhibition of the Extended-Spectrum beta-Lactamase PER-2 by Avibactam.
Resolution2.398 Å
Binding residue
(original residue number in PDB)
S70 W105 S130 N132 T235 G236 T237
Binding residue
(residue number reindexed from 1)
S47 W84 S111 N113 T216 G217 T218
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.70,Ki=20uM
Enzymatic activity
Catalytic site (original residue number in PDB) S70 K73 S130 E166 K234 T237
Catalytic site (residue number reindexed from 1) S47 K50 S111 E147 K215 T218
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

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Molecular Function

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Biological Process
External links
PDB RCSB:6d3g, PDBe:6d3g, PDBj:6d3g
PDBsum6d3g
PubMed31235626
UniProtA2RP81

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