Structure of PDB 1xmm Chain D Binding Site BS01

Receptor Information
>1xmm Chain D (length=292) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APVRLPFSGFRLQKVLRESARDKIIFLHGKVNEGDGEDAVVILEKTPFQV
EQVAQLLPELQLQFSDIYSTYHLFPPRQLNDVKTTVVYPATEKHLQKYLR
QDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPD
PSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNIL
HQGQEAILQRYRMKGDHLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERA
HLLAEVIENLECDPRHYQQRTLTFALRADDPLLKLLQEAQQS
Ligand information
Ligand IDM7G
InChIInChI=1S/C11H17N5O11P2/c1-15-3-16(8-5(15)9(19)14-11(12)13-8)10-7(18)6(17)4(26-10)2-25-29(23,24)27-28(20,21)22/h3-4,6-7,10,17-18H,2H2,1H3,(H5-,12,13,14,19,20,21,22,23,24)/p+1/t4-,6-,7-,10-/m1/s1
InChIKeySBASPRRECYVBRF-KQYNXXCUSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C[n+]1cn(c2c1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC1OC(n2c[n+](C)c3c2N=C(N)NC3=O)C(O)C1O
OpenEye OEToolkits 2.0.7C[n+]1cn(c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.385C[n+]1cn([CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O)c3N=C(N)NC(=O)c13
CACTVS 3.385C[n+]1cn([C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O)c3N=C(N)NC(=O)c13
FormulaC11 H18 N5 O11 P2
Name7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
ChEMBL
DrugBankDB01960
ZINCZINC000013548083
PDB chain1xmm Chain D Residue 404 [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]
PDB1xmm Crystal structures of human DcpS in ligand-free and m7GDP-bound forms suggest a dynamic mechanism for scavenger mRNA decapping.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		W175 E185 D205 L206 K207 H268 P271 S272 Y273 H277 H279 R294
Binding residue
(residue number reindexed from 1)		W130 E140 D160 L161 K162 H223 P226 S227 Y228 H232 H234 R249
Annotation score2
Enzymatic activity
Enzyme Commision number 3.6.1.59: 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase.
Gene Ontology
Molecular Function
GO:0000340 RNA 7-methylguanosine cap binding
GO:0004532 RNA exonuclease activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0042802 identical protein binding
GO:0140932 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity
Biological Process
GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0045292 mRNA cis splicing, via spliceosome
GO:0110156 mRNA methylguanosine-cap decapping
Cellular Component
GO:0000932 P-body
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1xmm, PDBe:1xmm, PDBj:1xmm
PDBsum1xmm
PubMed15769464
UniProtQ96C86|DCPS_HUMAN m7GpppX diphosphatase (Gene Name=DCPS)

[Back to BioLiP]