Structure of PDB 5n2v Chain B Binding Site BS04

Receptor Information
>5n2v Chain B (length=223) Species: 4896 (Schizosaccharomyces pombe) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFTNATFSQVLDDLSARFILNLPAEEQSSVERLCFQIEQAHWFYEDFIRA
QNDQLPSLGLRVFSAKLFAHCPLLWKWSKVHEEAFDDFLRYKTRIPVRGA
IMLDMSMQQCVLVKGWKASSGWGFPKGKIDKDESDVDCAIREVYEETGFD
CSSRINPNEFIDMTIRGQNVRLYIIPGISLDTRFESRTRKEISKIEWHNL
MDLPTFYMVIPFLAPLKKWIKKR
Ligand information
Ligand ID8NK
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 2.0.6C[n+]1cn(c2c1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O
OpenEye OEToolkits 2.0.6C[n+]1cn(c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=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
Name7-methylguanosine 5'-diphosphate
ChEMBL
DrugBank
ZINCZINC000015521877
PDB chain5n2v Chain B Residue 304 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5n2v Changes in conformational equilibria regulate the activity of the Dcp2 decapping enzyme.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		W43 D47 G128 K129 E143 R190 K191 E192
Binding residue
(residue number reindexed from 1)		W42 D46 G127 K128 E142 R189 K190 E191
Annotation score4
Enzymatic activity
Enzyme Commision number 3.-.-.-
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0016787 hydrolase activity
GO:0030145 manganese ion binding
GO:0140933 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
Biological Process
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5n2v, PDBe:5n2v, PDBj:5n2v
PDBsum5n2v
PubMed28533364
UniProtO13828|DCP2_SCHPO mRNA decapping complex subunit 2 (Gene Name=dcp2)

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