Structure of PDB 2xpk Chain A Binding Site BS01

Receptor Information

>2xpk 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
RSFAIYWDDIQDKSAAKHAQVLNRFNEEFVKAKGDVKPLITCPTEYDTGA
MVSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYDR
NMAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKI
SIHTAADYSWNMDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKT
WAKSGREDAPELRAKMDELWNKLSSKEDASALIEELYGEFARMEEACNNL
KANLPEVALEECSRQLDELITLAQGDKASLDMIVAQLNEDTEAYESAKEI
AQNKLNTALSSFAVISEKVAQSFIQEALSFDLTLI

Ligand information

Ligand ID

Z0M

InChI

InChI=1S/C19H25N3O4S/c23-11-14-17(25)18(26)16(21-15(24)8-9-27)19-20-13(10-22(14)19)7-6-12-4-2-1-3-5-12/h1-5,10,14,16-18,23,25-27H,6-9,11H2,(H,21,24)/t14-,16-,17-,18-/m1/s1

InChIKey

ZEEDRHPJCAOZKV-VDHUWJSZSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.6.1	c1ccc(cc1)CCc2cn3c(n2)[C@@H]([C@H]([C@@H]([C@H]3CO)O)O)NC(=O)CCS
CACTVS 3.352	OC[C@@H]1[C@@H](O)[C@H](O)[C@@H](NC(=O)CCS)c2nc(CCc3ccccc3)cn12
ACDLabs 10.04	O=C(NC2c1nc(cn1C(C(O)C2O)CO)CCc3ccccc3)CCS
CACTVS 3.352	OC[CH]1[CH](O)[CH](O)[CH](NC(=O)CCS)c2nc(CCc3ccccc3)cn12
OpenEye OEToolkits 1.6.1	c1ccc(cc1)CCc2cn3c(n2)C(C(C(C3CO)O)O)NC(=O)CCS

Formula

C19 H25 N3 O4 S

Name

N-[(5R,6R,7R,8S)-6,7-DIHYDROXY-5-(HYDROXYMETHYL)-2-(2-PHENYLETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDIN-8-YL]-3-SULFANYLPROPANAMIDE;
GLCNACSTATIN F

PDB chain

2xpk Chain A Residue 1625 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	2xpk Cell-Penetrant, Nanomolar O-Glcnacase Inhibitors Selective Against Lysosomal Hexosaminidases.
Resolution	2.4 Å
Binding residue (original residue number in PDB)	G187 K218 D297 D298 C331 Y335 V370 W394 D401
Binding residue (residue number reindexed from 1)	G148 K179 D258 D259 C292 Y296 V331 W355 D362
Annotation score	1
Binding affinity	MOAD: Ki=0.005nM PDBbind-CN: -logKd/Ki=11.30,Ki=0.005nM

Enzymatic activity

Enzyme Commision number

3.2.1.169: protein O-GlcNAcase.

External links

PDB	RCSB:2xpk, PDBe:2xpk, PDBj:2xpk
PDBsum	2xpk
PubMed	21095575
UniProt	Q0TR53\|OGA_CLOP1 O-GlcNAcase NagJ (Gene Name=nagJ)

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