Structure of PDB 5ne3 Chain B Binding Site BS01

Receptor Information
>5ne3 Chain B (length=269) Species: 522373 (Stenotrophomonas maltophilia K279a) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APTDAAITAASDFAALEKACAGRLGVTLLDTASGRRIGHRQDERFPMCST
FKSMLAATVLSQAERMPALLDRRVPVGEADLLSHAPVTRRHAGKDMTVRD
LCRATIITSDNTAANLLFGVVGGPPAVTAFLRASGDTVSRSDRLEPELNS
FAKGDPRDTTTPAAMAATLQRVVLGEVLQPASRQQLADWLIDNETGDACL
RAGLGKRWRVGDKTGSNGEDARNDIAVLWPVAGGAPWVLTAYLQAGAISY
EQRASVLAQVGRIADRLIG
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 chain5ne3 Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ne3 Structural/mechanistic insights into the efficacy of nonclassical beta-lactamase inhibitors against extensively drug resistant Stenotrophomonas maltophilia clinical isolates.
Resolution1.35 Å
Binding residue
(original residue number in PDB)
S69 H104 S129 N131 N169 T234 G235 S236
Binding residue
(residue number reindexed from 1)
S49 H84 S109 N111 N149 T214 G215 S216
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) S69 K72 S129 E165 K233 S236
Catalytic site (residue number reindexed from 1) S49 K52 S109 E145 K213 S216
Enzyme Commision number 3.5.2.6: beta-lactamase.
Gene Ontology
Molecular Function
GO:0008800 beta-lactamase activity
GO:0016787 hydrolase 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

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Biological Process
External links
PDB RCSB:5ne3, PDBe:5ne3, PDBj:5ne3
PDBsum5ne3
PubMed28876489
UniProtB2FRP5

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