Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T51565 Target Info
Target Name Casein kinase II alpha (CSNK2A1)
Synonyms Protein kinase CK2; Casein kinase II subunit alpha; CK2A1; CK II alpha; CK II
Target Type Clinical trial Target
Gene Name CSNK2A1
Biochemical Class Kinase
UniProt ID
CSK21_HUMAN
Ligand General Information  Top
Ligand Name Uridine-5'-Diphosphate Ligand Info
Canonical SMILES C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
InChI 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
InChIKey XCCTYIAWTASOJW-XVFCMESISA-N
PubChem Compound ID 6031
Drug Binding Sites of Target  Top
PDB ID: 4GYW      Crystal structure of human O-GlcNAc Transferase in complex with UDP and a glycopeptide
Method X-ray diffraction Resolution 1.70 Å Mutation No [1]
PDB Sequence
YPGGSTPVSS
22
ANMM
Residue
Distance (Å)
THR18
3.254
PRO19
3.644
Residue
Distance (Å)
VAL20
3.569
SER21
2.844
PDB ID: 3TAX      A Neutral Diphosphate Mimic Crosslinks the Active Site of Human O-GlcNAc Transferase
Method X-ray diffraction Resolution 1.88 Å Mutation No [2]
PDB Sequence
YPGGSTPVSS
22
ANMM
Residue
Distance (Å)
THR18
3.337
PRO19
3.658
Residue
Distance (Å)
VAL20
3.677
SER21
3.098
PDB ID: 4GZ3      Crystal structure of human O-GlcNAc Transferase with UDP and a thioglycopeptide
Method X-ray diffraction Resolution 1.90 Å Mutation No [1]
PDB Sequence
YPGGSTPVSS
22
ANMM
Residue
Distance (Å)
THR18
3.216
PRO19
3.629
Residue
Distance (Å)
VAL20
3.504
SER21
2.908
PDB ID: 3PE4      Structure of human O-GlcNAc transferase and its complex with a peptide substrate
Method X-ray diffraction Resolution 1.95 Å Mutation No [3]
PDB Sequence
YPGGSTPVSS
22
ANMM
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .B:18 or .B:19 or .B:20 or .B:21; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
THR18
3.321
PRO19
3.713
Residue
Distance (Å)
VAL20
3.613
SER21
2.995
PDB ID: 5HGV      Structure of an O-GlcNAc transferase point mutant, D554N in complex with peptide
Method X-ray diffraction Resolution 2.05 Å Mutation Yes [4]
PDB Sequence
YPGGSTPVSS
22
ANMM
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .B:18 or .B:19 or .B:20 or .B:21; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
THR18
3.240
PRO19
3.634
Residue
Distance (Å)
VAL20
3.230
SER21
2.967
PDB ID: 5VIF      Electrophilic probes for deciphering substrate recognition by O-GlcNAc transferase
Method X-ray diffraction Resolution 2.25 Å Mutation No [5]
PDB Sequence
YPGGSTPVSS
22
AN
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .B:18 or .B:19 or .B:20 or .B:21; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
THR18
3.251
PRO19
3.777
Residue
Distance (Å)
VAL20
3.586
SER21
2.845
PDB ID: 5VIE      Electrophilic probes for deciphering substrate recognition by O-GlcNAc transferase
Method X-ray diffraction Resolution 2.60 Å Mutation No [5]
PDB Sequence
YPGGSTPVSS
22
AN
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UDP or .UDP2 or .UDP3 or :3UDP;style chemicals stick;color identity;select .B:18 or .B:19 or .B:20 or .B:21; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
THR18
3.372
PRO19
3.673
Residue
Distance (Å)
VAL20
3.404
SER21
2.787
References  Top
REF 1 Structural snapshots of the reaction coordinate for O-GlcNAc transferase. Nat Chem Biol. 2012 Dec;8(12):966-8.
REF 2 A neutral diphosphate mimic crosslinks the active site of human O-GlcNAc transferase. Nat Chem Biol. 2011 Nov 13;8(1):72-7.
REF 3 Structure of human O-GlcNAc transferase and its complex with a peptide substrate. Nature. 2011 Jan 27;469(7331):564-7.
REF 4 How the glycosyltransferase OGT catalyzes amide bond cleavage. Nat Chem Biol. 2016 Nov;12(11):899-901.
REF 5 Electrophilic probes for deciphering substrate recognition by O-GlcNAc transferase. Nat Chem Biol. 2017 Dec;13(12):1267-1273.

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