Structure of PDB 3gdh Chain C Binding Site BS01

Receptor Information
>3gdh Chain C (length=207) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPELAKYWAQRYRLFSRFDDGIKLDREGWFSVTPEKIAEHIAGRVSQSFK
CDVVVDAFCGVGGNTIQFALTGMRVIAIDIDPVKIALARNNAEVYGIADK
IEFICGDFLLLASFLKADVVFLSPPWGGPDYATAETFDIRTMMSPDGFEI
FRLSKKITNNIVYFLPRNADIDQVASLAGPGGQVEIEQNFLNNKLKTITA
YFGDLIR
Ligand information
Ligand IDMGP
InChIInChI=1S/C11H18N5O14P3/c1-15-3-16(8-5(15)9(19)14-11(12)13-8)10-7(18)6(17)4(28-10)2-27-32(23,24)30-33(25,26)29-31(20,21)22/h3-4,6-7,10,17-18H,2H2,1H3,(H6-,12,13,14,19,20,21,22,23,24,25,26)/p+1/t4-,6-,7-,10-/m1/s1
InChIKeyDKVRNHPCAOHRSI-KQYNXXCUSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C[n+]1cn(c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341C[n+]1cn([C@@H]2O[C@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O)c3N=C(N)NC(=O)c13
OpenEye OEToolkits 1.5.0C[n+]1cn(c2c1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2c[n+](c1c2N=C(N)NC1=O)C)C(O)C3O
CACTVS 3.341C[n+]1cn([CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O)c3N=C(N)NC(=O)c13
FormulaC11 H19 N5 O14 P3
Name7-METHYL-GUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1234303
DrugBankDB02716
ZINCZINC000015601432
PDB chain3gdh Chain C Residue 3 [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]
PDB3gdh Structural basis for m7G-cap hypermethylation of small nuclear, small nucleolar and telomerase RNA by the dimethyltransferase TGS1.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		K646 F670 S671 V672 S763 P764 W766 G768 Y771 R807 K836
Binding residue
(residue number reindexed from 1)		K6 F30 S31 V32 S123 P124 W126 G128 Y131 R167 K196
Annotation score1
Enzymatic activity
Enzyme Commision number 2.1.1.-
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
Biological Process
GO:0001510 RNA methylation
GO:0036261 7-methylguanosine cap hypermethylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3gdh, PDBe:3gdh, PDBj:3gdh
PDBsum3gdh
PubMed19386620
UniProtQ96RS0|TGS1_HUMAN Trimethylguanosine synthase (Gene Name=TGS1)

[Back to BioLiP]