Structure of PDB 2vur Chain B Binding Site BS01

Receptor Information

>2vur Chain B (length=584) Species: 1502 (Clostridium perfringens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

VLVPNLNPTPENLEVVGDGFKITSSINLVGEEEADENAVNALREFLTANN
IEINSENDPNSTTLIIGEVDDDIPELDEALNGTTAENLKEEGYALVSNDG
KIAIEGKDGDGTFYGVQTFKQLVKESNIPEVNITDYPTVSARGIVEGFYG
TPWTHQDRLDQIKFYGENKLNTYIYAPKDDPYHREKWREPYPESEMQRMQ
ELINASAENKVDFVFGISPGIDIRFDGDAGEEDFNHLITKAESLYDMGVR
SFAIYWDDIQDKSAAKHAQVLNRFNEEFVKAKGDVKPLITVPTEYDTGAM
VSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYNRN
MAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKIS
IHTAADYSWNMDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKTW
AKSGREDAPELRAKMDELWNKLSSKEDASALIEELYGEFARMEEACNNLK
ANLPEVALEECSRQLDELITLAQGDKASLDMIVAQLNEDTEAYESAKEIA
QNKLNTALSSFAVISEKVAQSFIQEALSFDLTLI

Ligand information

Ligand ID

YX1

InChI

InChI=1S/C8H17N3O7/c1-11(10-17)8(16)9-4-6(14)5(13)3(2-12)18-7(4)15/h3-7,10,12-15,17H,2H2,1H3,(H,9,16)/t3-,4-,5-,6-,7-/m1/s1

InChIKey

LUNQAAUVSFIVKD-NYMZXIIRSA-N

SMILES

Software	SMILES
CACTVS 3.341	CN(NO)C(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]1O
ACDLabs 10.04	O=C(NC1C(O)C(O)C(OC1O)CO)N(NO)C
OpenEye OEToolkits 1.5.0	CN(C(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@H]1O)CO)O)O)NO
OpenEye OEToolkits 1.5.0	CN(C(=O)NC1C(C(C(OC1O)CO)O)O)NO
CACTVS 3.341	CN(NO)C(=O)N[CH]1[CH](O)O[CH](CO)[CH](O)[CH]1O

Formula

C8 H17 N3 O7

Name

2-deoxy-2-{[(2-hydroxy-1-methylhydrazino)carbonyl]amino}-beta-D-glucopyranose;
2-deoxy-2-{[(2-hydroxy-1-methylhydrazino)carbonyl]amino}-beta-D-glucose;
2-deoxy-2-{[(2-hydroxy-1-methylhydrazino)carbonyl]amino}-D-glucose;
2-deoxy-2-{[(2-hydroxy-1-methylhydrazino)carbonyl]amino}-glucose

PDB chain

2vur Chain B Residue 1626 [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	2vur Chemical Dissection of the Link between Streptozotocin, O-Glcnac, and Pancreatic Cell Death.
Resolution	2.2 Å
Binding residue (original residue number in PDB)	D297 V331 Y335 V370 W394 D401 Y402
Binding residue (residue number reindexed from 1)	D257 V291 Y295 V330 W354 D361 Y362
Annotation score	1
Binding affinity	MOAD: ic50=30uM

Enzymatic activity

Enzyme Commision number

3.2.1.169: protein O-GlcNAcase.

External links

PDB	RCSB:2vur, PDBe:2vur, PDBj:2vur
PDBsum	2vur
PubMed	18721751
UniProt	Q0TR53\|OGA_CLOP1 O-GlcNAcase NagJ (Gene Name=nagJ)

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