Structure of PDB 5ne1 Chain B Binding Site BS01

Receptor Information
>5ne1 Chain B (length=270) Species: 40324 (Stenotrophomonas maltophilia) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NAPTDAAITAASDFAALEKACAGRLGVTLLDTASGRRIGHRQDERFPMCS
TFKSMLAATVLSQAERMPALLDRRVPVGEADLLSHAPVTRRHAGKDMTVR
DLCRATIITSDNTAANLLFGVVGGPPAVTAFLRASGDTVSRSDRLEPELN
SFAKGDPRDTTTPAAMAATLQRVVLGEVLQPASRQQLADWLIDNETGDAC
LRAGLGKRWRVGDKTGSNGEDARNDIAVLWPVAGGAPWVLTAYLQAGAIS
YEQRASVLAQVGRIADRLIG
Ligand information
Ligand IDOK3
InChIInChI=1S/C17H18BN2O6/c19-9-10-4-6-11(7-5-10)16(21)20-14-8-12-2-1-3-13(17(22)23)15(12)26-18(14,24)25/h1-7,14,24-25H,8-9,19H2,(H,20,21)(H,22,23)/q-1/t14-/m0/s1
InChIKeyQLXKUYDHLJOWQG-AWEZNQCLSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NCc1ccc(cc1)C(=O)N[C@H]2Cc3cccc(C(O)=O)c3O[B-]2(O)O
OpenEye OEToolkits 2.0.7[B-]1(C(Cc2cccc(c2O1)C(=O)O)NC(=O)c3ccc(cc3)CN)(O)O
OpenEye OEToolkits 2.0.7[B-]1([C@H](Cc2cccc(c2O1)C(=O)O)NC(=O)c3ccc(cc3)CN)(O)O
CACTVS 3.385NCc1ccc(cc1)C(=O)N[CH]2Cc3cccc(C(O)=O)c3O[B-]2(O)O
FormulaC17 H18 B N2 O6
Name(4~{R})-4-[[4-(aminomethyl)phenyl]carbonylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid
ChEMBLCHEMBL4461260
DrugBank
ZINC
PDB chain5ne1 Chain B Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5ne1 Structural/mechanistic insights into the efficacy of nonclassical beta-lactamase inhibitors against extensively drug resistant Stenotrophomonas maltophilia clinical isolates.
Resolution2.09 Å
Binding residue
(original residue number in PDB)		S70 H105 S130 N132 N170 T235 G236 S237 N238 G240
Binding residue
(residue number reindexed from 1)		S50 H85 S110 N112 N150 T215 G216 S217 N218 G219
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.28,IC50=5.25nM
Enzymatic activity
Catalytic site (original residue number in PDB) S70 K73 S130 E166 K234 S237
Catalytic site (residue number reindexed from 1) S50 K53 S110 E146 K214 S217
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
View graph for
Biological Process
External links
PDB RCSB:5ne1, PDBe:5ne1, PDBj:5ne1
PDBsum5ne1
PubMed28876489
UniProtQ9RBQ1

[Back to BioLiP]