Structure of PDB 5vfd Chain A Binding Site BS02

Receptor Information
>5vfd Chain A (length=244) Species: 470 (Acinetobacter baumannii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPAS
TFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVP
VYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVN
FADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGW
LTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII
Ligand information
Ligand ID9CM
InChIInChI=1S/C8H11N3O6S/c1-4-2-5(7(9)12)10-3-6(4)11(8(10)13)17-18(14,15)16/h2,5-6H,3H2,1H3,(H2,9,12)(H,14,15,16)/t5-,6-/m0/s1
InChIKeyWHFPRPRSXFJXMN-WDSKDSINSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC1=C[C@H](N2C[C@@H]1N(C2=O)OS(=O)(=O)O)C(=O)N
OpenEye OEToolkits 2.0.6CC1=CC(N2CC1N(C2=O)OS(=O)(=O)O)C(=O)N
CACTVS 3.385CC1=C[C@H]([N@]2C[C@@H]1N(O[S](O)(=O)=O)C2=O)C(N)=O
ACDLabs 12.01C1(=CC(C(N)=O)N2CC1N(C2=O)OS(=O)(O)=O)C
CACTVS 3.385CC1=C[CH]([N]2C[CH]1N(O[S](O)(=O)=O)C2=O)C(N)=O
FormulaC8 H11 N3 O6 S
Name(2S,5R)-4-methyl-7-oxo-6-(sulfooxy)-1,6-diazabicyclo[3.2.1]oct-3-ene-2-carboxamide
ChEMBLCHEMBL3140306
DrugBank
ZINCZINC000103245006
PDB chain5vfd Chain A Residue 307 [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]
PDB5vfd ETX2514 is a broad-spectrum beta-lactamase inhibitor for the treatment of drug-resistant Gram-negative bacteria including Acinetobacter baumannii.
Resolution1.93 Å
Binding residue
(original residue number in PDB)		Y112 P113 M114 W115 L127
Binding residue
(residue number reindexed from 1)		Y81 P82 M83 W84 L96
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.44,IC50=0.36uM
Enzymatic activity
Catalytic site (original residue number in PDB) S81 K84 S128 Y133 W167 W221
Catalytic site (residue number reindexed from 1) S50 K53 S97 Y102 W136 W190
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0008658 penicillin binding
GO:0008800 beta-lactamase activity
GO:0016787 hydrolase activity
Biological Process
GO:0071555 cell wall organization

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5vfd, PDBe:5vfd, PDBj:5vfd
PDBsum5vfd
PubMed28665414
UniProtQ8RLA6

[Back to BioLiP]