Structure of PDB 3gs6 Chain A Binding Site BS01

Receptor Information
>3gs6 Chain A (length=322) Species: 666 (Vibrio cholerae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MGPLWLDVAGYELSAEDRAILAHPTVGGVILFGRNYHDNQQLLALNKAIR
QAAARPILIGVDQEGGRVQRFREGFSRIPPAQYYARAENGVELAEQGGWL
MAAELIAHDVDLSFAPVLDMGFACKAIGNRAFGEDVQTVLKHSSAFLRGM
KAVGMATTGKHFPGHGAVIHLETPYDERETIAQDMAIFRAQIEAGVLDAM
MPAHVVYPHYDAQPASGSSYWLKQVLREELGFKGIVFSDDLSMVMGGPVE
RSHQALVAGCDMILICNKREAAVEVLDNLPIMEVPQAEALLKKQQFSYSE
LKRLERWQQASANMQRLIEQFS
Ligand information
Ligand IDNP6
InChIInChI=1S/C17H23N3O7/c1-2-6-12(22)19-13-15(24)14(23)11(9-21)26-16(13)20-27-17(25)18-10-7-4-3-5-8-10/h3-5,7-8,11,13-15,21,23-24H,2,6,9H2,1H3,(H,18,25)(H,19,22)/b20-16-/t11-,13-,14-,15-/m1/s1
InChIKeyITVRELFVFCOUMV-ZVZWZHPPSA-N
SMILES
SoftwareSMILES
CACTVS 3.352CCCC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)OC1=NOC(=O)Nc2ccccc2
OpenEye OEToolkits 1.6.1CCCC(=O)NC1C(C(C(OC1=NOC(=O)Nc2ccccc2)CO)O)O
ACDLabs 10.04O=C(O\N=C1/OC(CO)C(O)C(O)C1NC(=O)CCC)Nc2ccccc2
OpenEye OEToolkits 1.6.1CCCC(=O)N[C@@H]\1[C@H]([C@@H]([C@H](O/C1=N\OC(=O)Nc2ccccc2)CO)O)O
CACTVS 3.352CCCC(=O)N[C@@H]\1[C@@H](O)[C@H](O)[C@@H](CO)OC\1=N\OC(=O)Nc2ccccc2
FormulaC17 H23 N3 O7
Name[[(3R,4R,5S,6R)-3-(BUTANOYLAMINO)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)OXAN-2-YLIDENE]AMINO] N-PHENYLCARBAMATE
ChEMBLCHEMBL255476
DrugBankDB07432
ZINCZINC000034600850
PDB chain3gs6 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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PDB3gs6 Insight into a strategy for attenuating AmpC-mediated beta-lactam resistance: structural basis for selective inhibition of the glycoside hydrolase NagZ.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		I30 D62 R130 K160 H161 H165 M204 M246
Binding residue
(residue number reindexed from 1)		I30 D62 R130 K160 H161 H165 M201 M243
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.59,Ki=0.26uM
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:3gs6, PDBe:3gs6, PDBj:3gs6
PDBsum3gs6
PubMed19499593
UniProtQ9KU37|NAGZ_VIBCH Beta-hexosaminidase (Gene Name=nagZ)

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