Structure of PDB 5vif Chain A Binding Site BS03

Receptor Information

>5vif Chain A (length=683) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

LANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALM
HYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAH
SNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDY
DERMKKLVSIVADQLEKNRLPSVHPHHSMLYPLSHGFRKAIAERHGNLCL
DKINVLHKPPYEHPKDLKLSDGRLRVGYVSSDFGNHPTSHLMQSIPGMHN
PDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQIPCNGKAADRIHQDG
IHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALFMDYIITDQE
TSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDFHIYDNRIVL
NGIDLKAFLDSLPDVKIVNMPVIPMNTIAEAVIEMINRGQIQITINGFSI
SNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAIVYCNFNQLYKID
PSTLQMWANILKRVPNSVLWLLRFPAVGEPNIQQYAQNMGLPQNRIIFSP
VAPKEEHVRRGQLADVCLDTPLCNGHTTGMDVLWAGTPMVTMPGETLASR
VAASQLTCLGCLELIAKNRQEYEDIAVKLGTDLEYLKKVRGKVWKQRISS
PLFNTKQYTMELERLYLQMWEHYAAGNKPDHMI

Ligand information

Ligand ID

9C1

InChI

InChI=1S/C10H16ClNO6/c11-3-1-2-6(14)12-7-9(16)8(15)5(4-13)18-10(7)17/h1-2,5,7-10,13,15-17H,3-4H2,(H,12,14)/b2-1+/t5-,7-,8-,9-,10-/m1/s1

InChIKey

LKECTNVLFDGIBK-KKRTVAFTSA-N

SMILES

Software	SMILES
CACTVS 3.385	OC[CH]1O[CH](O)[CH](NC(=O)C=CCCl)[CH](O)[CH]1O
OpenEye OEToolkits 2.0.6	C(C=CC(=O)NC1C(C(C(OC1O)CO)O)O)Cl
ACDLabs 12.01	C(=C/CCl)\C(=O)NC1C(C(C(CO)OC1O)O)O
OpenEye OEToolkits 2.0.6	C(/C=C/C(=O)N[C@@H]1[C@H]([C@@H]([C@H](OC1O)CO)O)O)Cl
CACTVS 3.385	OC[C@H]1O[C@@H](O)[C@H](NC(=O)\C=C\CCl)[C@@H](O)[C@@H]1O

Formula

C10 H16 Cl N O6

Name

2-{[(2E)-4-chlorobut-2-enoyl]amino}-2-deoxy-beta-D-glucopyranose;
2-{[(2E)-4-chlorobut-2-enoyl]amino}-2-deoxy-beta-D-glucose;
2-{[(2E)-4-chlorobut-2-enoyl]amino}-2-deoxy-D-glucose;
2-{[(2E)-4-chlorobut-2-enoyl]amino}-2-deoxy-glucose

ChEMBL

DrugBank

ZINC

PDB chain

5vif Chain B Residue 101 [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	5vif Electrophilic probes for deciphering substrate recognition by O-GlcNAc transferase.
Resolution	2.25 Å
Binding residue (original residue number in PDB)	H498 P559 T560 L653 P656 F694 Y841 C917 H920 T921
Binding residue (residue number reindexed from 1)	H176 P237 T238 L331 P334 F372 Y497 C573 H576 T577
Annotation score	1

Enzymatic activity

Enzyme Commision number

2.4.1.255: protein O-GlcNAc transferase.

External links

PDB	RCSB:5vif, PDBe:5vif, PDBj:5vif
PDBsum	5vif
PubMed	29058723
UniProt	O15294\|OGT1_HUMAN UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (Gene Name=OGT)

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