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BioLiP

Structure of PDB 2cbj Chain A Binding Site BS01

Receptor Information
>2cbj Chain A (length=585) Species: 1502 (Clostridium perfringens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QVLVPNLNPTPENLEVVGDGFKITSSINLVGEEEADENAVNALREFLTAN
NIEINSENDPNSTTLIIGEVDDDIPELDEALNGTTAENLKEEGYALVSND
GKIAIEGKDGDGTFYGVQTFKQLVKESNIPEVNITDYPTVSARGIVEGFY
GTPWTHQDRLDQIKFYGENKLNTYIYAPKDDPYHREKWREPYPESEMQRM
QELINASAENKVDFVFGISPGIDIRFDGDAGEEDFNHLITKAESLYDMGV
RSFAIYWDDIQDKSAAKHAQVLNRFNEEFVKAKGDVKPLITVPTEYDTGA
MVSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYNR
NMAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKI
SIHTAADYSWNMDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKT
WAKSGREDAPELRAKMDELWNKLSSKEDASALIEELYGEFARMEEACNNL
KANLPEVALEECSRQLDELITLAQGDKASLDMIVAQLNEDTEAYESAKEI
AQNKLNTALSSFAVISEKVAQSFIQEALSFDLTLI
Ligand information
Ligand IDOAN
InChIInChI=1S/C15H19N3O7/c1-8(20)16-11-13(22)12(21)10(7-19)24-14(11)18-25-15(23)17-9-5-3-2-4-6-9/h2-6,10-13,19,21-22H,7H2,1H3,(H,16,20)(H,17,23)/b18-14-/t10-,11-,12-,13-/m1/s1
InChIKeyPBLNJFVQMUMOJY-JXZOILRNSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC(=O)N[C@@H]\1[C@@H](O)[C@H](O)[C@@H](CO)OC\1=N\OC(=O)Nc2ccccc2
OpenEye OEToolkits 1.7.2CC(=O)NC1C(C(C(OC1=NOC(=O)Nc2ccccc2)CO)O)O
OpenEye OEToolkits 1.7.2CC(=O)N[C@@H]\1[C@H]([C@@H]([C@H](O/C1=N\OC(=O)Nc2ccccc2)CO)O)O
CACTVS 3.370CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)OC1=NOC(=O)Nc2ccccc2
ACDLabs 12.01O=C(O\N=C1/OC(CO)C(O)C(O)C1NC(=O)C)Nc2ccccc2
FormulaC15 H19 N3 O7
NameO-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE) AMINO-N-PHENYLCARBAMATE;
PUGNAc
ChEMBLCHEMBL404482
DrugBank
ZINCZINC000038599450
PDB chain2cbj Chain A Residue 1625 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2cbj Structural insights into the mechanism and inhibition of eukaryotic O-GlcNAc hydrolysis.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		G187 K218 D297 D298 Y335 V370 W394 N396 D401 Y402 W490
Binding residue
(residue number reindexed from 1)		G148 K179 D258 D259 Y296 V331 W355 N357 D362 Y363 W451
Annotation score1
Binding affinityMOAD: Ki=5.4nM
PDBbind-CN: -logKd/Ki=8.27,Ki=5.4nM
Enzymatic activity
Enzyme Commision number 3.2.1.169: protein O-GlcNAcase.
External links
PDB RCSB:2cbj, PDBe:2cbj, PDBj:2cbj
PDBsum2cbj
PubMed16541109
UniProtQ0TR53|OGA_CLOP1 O-GlcNAcase NagJ (Gene Name=nagJ)

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