Structure of PDB 5vif Chain A Binding Site BS02

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 IDUDP
InChIInChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyXCCTYIAWTASOJW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.370O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
FormulaC9 H14 N2 O12 P2
NameURIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL130266
DrugBankDB03435
ZINCZINC000004490939
PDB chain5vif Chain A Residue 1100 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5vif Electrophilic probes for deciphering substrate recognition by O-GlcNAc transferase.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		K842 L866 F868 V895 A896 K898 H901 H920 T921 T922 D925
Binding residue
(residue number reindexed from 1)		K498 L522 F524 V551 A552 K554 H557 H576 T577 T578 D581
Annotation score3
Binding affinityBindingDB: IC50=1800nM
Enzymatic activity
Enzyme Commision number 2.4.1.255: protein O-GlcNAc transferase.
External links
PDB RCSB:5vif, PDBe:5vif, PDBj:5vif
PDBsum5vif
PubMed29058723
UniProtO15294|OGT1_HUMAN UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (Gene Name=OGT)

[Back to BioLiP]