Structure of PDB 5utr Chain A Binding Site BS01

Receptor Information
>5utr Chain A (length=339) Species: 95486 (Burkholderia cenocepacia) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TTPGPVMLDVVGTTLSRDDARRLAHPNTGGVILFARHFQNRAQLTALTDS
IRAVREDILIAVDHEGGRVQRFRTDGFTVLPAMRRLGELWDRDVLLATKV
ATAVGYILAAELRACGIDMSFTPVLDLDYGHSKVIGDRAFHRDPRVVTLL
AKSLNHGLSLAGMANCGKHFPGHGFAEADSHVALPTDDRTLDAILEQDVA
PYDWLGLSLAAVIPAHVIYTQVDKRPAGFSRVWLQDILRGKLGFTGAIFS
DDLSMEAAREGGTLTQAADAALAAGCDMVLVCNQPDAAEVVLNGLKARAS
AESVRRIKRMRARGKALKWDKLIAQPEYLQAQALLSSAL
Ligand information
Ligand ID8MP
InChIInChI=1S/C10H20N2O4/c1-2-3-8(14)12-6-4-11-5-7(13)10(16)9(6)15/h6-7,9-11,13,15-16H,2-5H2,1H3,(H,12,14)/t6-,7-,9+,10+/m0/s1
InChIKeySWEITPYHDWSHKI-AKEJEFCPSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C(C(NC1CNCC(C(C1O)O)O)=O)CC
CACTVS 3.385CCCC(=O)N[C@H]1CNC[C@H](O)[C@@H](O)[C@@H]1O
CACTVS 3.385CCCC(=O)N[CH]1CNC[CH](O)[CH](O)[CH]1O
OpenEye OEToolkits 2.0.6CCCC(=O)N[C@H]1CNC[C@@H]([C@H]([C@@H]1O)O)O
OpenEye OEToolkits 2.0.6CCCC(=O)NC1CNCC(C(C1O)O)O
FormulaC10 H20 N2 O4
NameN-[(3S,4R,5R,6S)-4,5,6-trihydroxyazepan-3-yl]butanamide
ChEMBL
DrugBank
ZINC
PDB chain5utr Chain A Residue 401 [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]
PDB5utr Conformational flexibility of the glycosidase NagZ allows it to bind structurally diverse inhibitors to suppress beta-lactam antibiotic resistance.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		D65 V136 R140 K170 H171 S182 H183 D253 M257
Binding residue
(residue number reindexed from 1)		D63 V134 R138 K168 H169 S180 H181 D251 M255
Annotation score1
Binding affinityMOAD: Kd=7uM
Enzymatic activity
Enzyme Commision number 3.2.1.52: beta-N-acetylhexosaminidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004563 beta-N-acetylhexosaminidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0009254 peptidoglycan turnover
GO:0051301 cell division
GO:0071555 cell wall organization
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5utr, PDBe:5utr, PDBj:5utr
PDBsum5utr
PubMed28370529
UniProtB4EA43

[Back to BioLiP]