Structure of PDB 1st0 Chain B Binding Site BS02

Receptor Information
>1st0 Chain B (length=297) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VRLPFSGFRLQKVLRESARDKIIFLHGKVNEASGDGDGEDAVVILEKTPF
QVEQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLNDVKTTVVYPATEKH
LQKYLRQDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEADRI
VFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLP
LLRNILHQGQEAILQRYRMKGDHLRVYLHYLPSYYHLNVHFTALGFEAPG
SGVERAHLLAEVIENLECDPRHYQQRTLTFALRADDPLLKLLQEAQQ
Ligand information
Ligand IDGTG
InChIInChI=1S/C21H29N10O18P3/c1-29-5-31(15-9(29)17(37)28-21(23)26-15)19-13(35)11(33)7(47-19)3-45-51(40,41)49-52(42,43)48-50(38,39)44-2-6-10(32)12(34)18(46-6)30-4-24-8-14(30)25-20(22)27-16(8)36/h4-7,10-13,18-19,32-35H,2-3H2,1H3,(H8-,22,23,25,26,27,28,36,37,38,39,40,41,42,43)/p+1/t6-,7-,10-,11-,12-,13-,18-,19-/m1/s1
InChIKeyFHHZHGZBHYYWTG-INFSMZHSSA-O
SMILES
SoftwareSMILES
CACTVS 3.385C[n+]1cn([C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5C(=O)NC(=Nc45)N)[C@@H](O)[C@H]2O)c6N=C(N)NC(=O)c16
CACTVS 3.385C[n+]1cn([CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5C(=O)NC(=Nc45)N)[CH](O)[CH]2O)c6N=C(N)NC(=O)c16
OpenEye OEToolkits 1.7.5C[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[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5N=C(NC6=O)N)O)O)O)O
ACDLabs 10.04O=C1NC(=Nc2c1[n+](cn2C3OC(C(O)C3O)COP(=O)(O)OP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c5N=C(N)NC4=O)C(O)C6O)C)N
OpenEye OEToolkits 1.7.5C[n+]1cn(c2c1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5N=C(NC6=O)N)O)O)O)O
FormulaC21 H30 N10 O18 P3
Name7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE;
MRNA CAP ANALOG N7-METHYL GPPPG
ChEMBL
DrugBankDB03958
ZINCZINC000085547903
PDB chain1st0 Chain A Residue 651 [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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PDB1st0 Insights into the structure, mechanism, and regulation of scavenger mRNA decapping activity
Resolution1.9 Å
Binding residue
(original residue number in PDB)		F108 Y113
Binding residue
(residue number reindexed from 1)		F69 Y74
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

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1st0, PDBe:1st0, PDBj:1st0
PDBsum1st0
PubMed15068804
UniProtQ96C86|DCPS_HUMAN m7GpppX diphosphatase (Gene Name=DCPS)

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