Structure of PDB 5utp Chain B Binding Site BS01

Receptor Information
>5utp Chain B (length=335) Species: 95486 (Burkholderia cenocepacia) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KTTPGPVMLDVVGTTLSRDDARRLAHPNTGGVILFARHFQNRAQLTALTD
SIRAVREDILIAVDHEGGRVQRFRTDGFTVLPAMRRLGELWDRDVLLATK
VATAVGYILAAELRACGIDMSFTPVLDLDYGHSKVIGDRAFHRDPRVVTL
LAKSLNHGLSLAGMANCGKHFPGHGFAELPTDDRTLDAILEQDVAPYDWL
GLSLAAVIPAHVIYTQVDKRPAGFSRVWLQDILRGKLGFTGAIFSDDLSM
EAAREGGTLTQAADAALAAGCDMVLVCNQPDAAEVVLNGLKARASAESVR
RIKRMRARGKALKWDKLIAQPEYLQAQALLSSALA
Ligand information
Ligand ID8M7
InChIInChI=1S/C19H27N3O7/c1-3-11(4-2)17(26)21-14-16(25)15(24)13(10-23)28-18(14)22-29-19(27)20-12-8-6-5-7-9-12/h5-9,11,13-16,23-25H,3-4,10H2,1-2H3,(H,20,27)(H,21,26)/b22-18-/t13-,14-,15-,16-/m1/s1
InChIKeyILCJHDDOBKGXME-OXSJTRRESA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C(C)C(CC)C(NC\1C(C(O)C(CO)OC/1=N/OC(Nc2ccccc2)=O)O)=O
CACTVS 3.385CCC(CC)C(=O)N[C@@H]/1[C@@H](O)[C@H](O)[C@@H](CO)OC/1=N/OC(=O)Nc2ccccc2
OpenEye OEToolkits 2.0.6CCC(CC)C(=O)N[C@@H]\1[C@H]([C@@H]([C@H](O/C1=N\OC(=O)Nc2ccccc2)CO)O)O
CACTVS 3.385CCC(CC)C(=O)N[CH]1[CH](O)[CH](O)[CH](CO)OC1=NOC(=O)Nc2ccccc2
OpenEye OEToolkits 2.0.6CCC(CC)C(=O)NC1C(C(C(OC1=NOC(=O)Nc2ccccc2)CO)O)O
FormulaC19 H27 N3 O7
NameN-[(2Z,3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(phenylcarbamoyl)oxy]imino}tetrahydro-2H-pyran-3-yl]-2-ethylbutanamide
ChEMBLCHEMBL254583
DrugBank
ZINCZINC000040616211
PDB chain5utp Chain B Residue 901 [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]
PDB5utp Conformational flexibility of the glycosidase NagZ allows it to bind structurally diverse inhibitors to suppress beta-lactam antibiotic resistance.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		D65 R140 K170 H171 H175 D253 D254 M257
Binding residue
(residue number reindexed from 1)		D64 R139 K169 H170 H174 D246 D247 M250
Annotation score1
Binding affinityMOAD: Ki=3uM
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:5utp, PDBe:5utp, PDBj:5utp
PDBsum5utp
PubMed28370529
UniProtB4EA43

[Back to BioLiP]