Structure of PDB 3gsm Chain A Binding Site BS01

Receptor Information
>3gsm Chain A (length=324) Species: 666 (Vibrio cholerae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MGPLWLDVAGYELSAEDRAILAHPTVGGVILFGRNYHDNQQLLALNKAIR
QAAARPILIGVDQEGGRVQRFREGFSRIPPAQYYARAENGVELAEQGGWL
MAAELIAHDVDLSFAPVLDMGFACKAIGNRAFGEDVQTVLKHSSAFLRGM
KAVGMATTGKHFPGHGAVIADHLETPYDERETIAQDMAIFRAQIEAGVLD
AMMPAHVVYPHYDAQPASGSSYWLKQVLREELGFKGIVFSDDLSMVMGGP
VERSHQALVAGCDMILICNKREAAVEVLDNLPIMEVPQAEALLKKQQFSY
SELKRLERWQQASANMQRLIEQFS
Ligand information
Ligand IDVPU
InChIInChI=1S/C18H25N3O7/c1-2-3-9-13(23)20-14-16(25)15(24)12(10-22)27-17(14)21-28-18(26)19-11-7-5-4-6-8-11/h4-8,12,14-16,22,24-25H,2-3,9-10H2,1H3,(H,19,26)(H,20,23)/b21-17-/t12-,14-,15-,16-/m1/s1
InChIKeyNUNQIQQEEPOGDJ-JDOAOKHLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCCCC(=O)N[C@@H]\1[C@H]([C@@H]([C@H](O/C1=N\OC(=O)Nc2ccccc2)CO)O)O
ACDLabs 10.04O=C(O\N=C1/OC(CO)C(O)C(O)C1NC(=O)CCCC)Nc2ccccc2
CACTVS 3.341CCCCC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)OC1=NOC(=O)Nc2ccccc2
OpenEye OEToolkits 1.5.0CCCCC(=O)NC1C(C(C(OC1=NOC(=O)Nc2ccccc2)CO)O)O
CACTVS 3.341CCCCC(=O)N[C@@H]\1[C@@H](O)[C@H](O)[C@@H](CO)OC\1=N\OC(=O)Nc2ccccc2
FormulaC18 H25 N3 O7
Name[[(3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-(pentanoylamino)oxan-2-ylidene]amino] N-phenylcarbamate;
N-Valeryl-PUGNAc
ChEMBLCHEMBL256732
DrugBankDB08704
ZINCZINC000035859848
PDB chain3gsm Chain A Residue 341 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3gsm Insight into a strategy for attenuating AmpC-mediated beta-lactam resistance: structural basis for selective inhibition of the glycoside hydrolase NagZ.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		D62 R130 K160 H161 M204
Binding residue
(residue number reindexed from 1)		D62 R130 K160 H161 M203
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.48,Ki=0.33uM
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:0046677 response to antibiotic
GO:0051301 cell division
GO:0071555 cell wall organization
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3gsm, PDBe:3gsm, PDBj:3gsm
PDBsum3gsm
PubMed19499593
UniProtQ9KU37|NAGZ_VIBCH Beta-hexosaminidase (Gene Name=nagZ)

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