Structure of PDB 6ibo Chain A Binding Site BS02

Receptor Information
>6ibo Chain A (length=695) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
THADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQ
GKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQI
NPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQ
IVCDWTDYDERMKKLVSIVADQLEKNRLPSVHPHHSMLYPLSHGFRKAIA
ERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRVGYVSSDFGKHPTSHLM
QSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQIPCNGKA
ADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALFM
DYIITDQETSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDFK
SIYDNRIVLNGIDLKAFLDSLPDVKIVKMLNMPVIPMNTIAEAVIEMINR
GQIQITINGFSISNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAI
VYCNFNQLYKIDPSTLQMWANILKRVPNSVLWLLRFPAVGEPNIQQYAQN
MGLPQNRIIFSPVAPKEEHVRRGQLADVCLDTPLCNGHTTGMDVLWAGTP
MVTMPGETLASRVAASQLTCLGCLELIAKNRQEYEDIAVKLGTDLEYLKK
VRGKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMI
Ligand information
Ligand ID12V
InChIInChI=1S/C17H27N3O16P2S/c1-6(22)18-10-13(26)12(25)8(4-21)39-16(10)35-38(31,32)36-37(29,30)33-5-7-11(24)14(27)15(34-7)20-3-2-9(23)19-17(20)28/h2-3,7-8,10-16,21,24-27H,4-5H2,1H3,(H,18,22)(H,29,30)(H,31,32)(H,19,23,28)/t7-,8-,10-,11-,12-,13-,14-,15-,16+/m1/s1
InChIKeyJPRVHSQHWXZSNC-UBDZBXRQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](S[C@@H]1OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)CO)O)O
ACDLabs 12.01O=P(OC1SC(C(O)C(O)C1NC(=O)C)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
CACTVS 3.370CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)S[CH]1O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O
OpenEye OEToolkits 1.7.6CC(=O)NC1C(C(C(SC1OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)CO)O)O
CACTVS 3.370CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)S[C@@H]1O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O
FormulaC17 H27 N3 O16 P2 S
Name(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate;
URIDINE DIPHOSPHO-5-THIO-N-ACETYLGLUCOSAMINE
ChEMBLCHEMBL3596221
DrugBank
ZINCZINC000098207912
PDB chain6ibo Chain A Residue 1101 [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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PDB6ibo Catalytic deficiency of O-GlcNAc transferase leads to X-linked intellectual disability.
Resolution2.17 Å
Binding residue
(original residue number in PDB)
H506 H508 P569 T570 T643 L663 G664 P666 F704 K852 V905 A906 K908 H911 H930 T931 T932 D935
Binding residue
(residue number reindexed from 1)
H182 H184 P245 T246 T319 L339 G340 P342 F380 K510 V563 A564 K566 H569 H588 T589 T590 D593
Annotation score2
Enzymatic activity
Enzyme Commision number 2.4.1.255: protein O-GlcNAc transferase.
External links
PDB RCSB:6ibo, PDBe:6ibo, PDBj:6ibo
PDBsum6ibo
PubMed31296563
UniProtO15294|OGT1_HUMAN UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (Gene Name=OGT)

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