Structure of PDB 1st4 Chain A Binding Site BS01

Receptor Information
>1st4 Chain A (length=300) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APVRLPFSGFRLQKVLRESARDKIIFLHGKVNEASGDGDGEDAVVILEKT
PFQVEQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLNDVKTTVVYPATE
KHLQKYLRQDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEAD
RIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEH
LPLLRNILHQGQEAILQRYRMKGDHLRVYLHYLPSYYHLNVHFTALGFEA
PGSGVERAHLLAEVIENLECDPRHYQQRTLTFALRADDPLLKLLQEAQQS
Ligand information
Ligand IDGTA
InChIInChI=1S/C21H29N10O17P3/c1-29-6-31(17-10(29)18(36)28-21(23)27-17)20-14(35)12(33)8(46-20)3-44-50(39,40)48-51(41,42)47-49(37,38)43-2-7-11(32)13(34)19(45-7)30-5-26-9-15(22)24-4-25-16(9)30/h4-8,11-14,19-20,32-35H,2-3H2,1H3,(H7-,22,23,24,25,27,28,36,37,38,39,40,41,42)/p+1/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1
InChIKeyQQOHNVHGNZYSBP-XPWFQUROSA-O
SMILES
SoftwareSMILES
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)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O
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)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)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)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O)c6N=C(N)NC(=O)c16
CACTVS 3.341C[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(N)ncnc45)[CH](O)[CH]2O)c6N=C(N)NC(=O)c16
ACDLabs 10.04O=C1NC(=Nc2c1[n+](cn2C3OC(C(O)C3O)COP(=O)(O)OP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)N
FormulaC21 H30 N10 O17 P3
NameP1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE;
7-METHYL-GPPPA
ChEMBL
DrugBankDB01649
ZINCZINC000096006025
PDB chain1st4 Chain A Residue 451 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1st4 Insights into the structure, mechanism, and regulation of scavenger mRNA decapping activity
Resolution2.02 Å
Binding residue
(original residue number in PDB)		F63 I83 Y143 W175 E185 D205 L206 K207 H268 S272 Y273 N277 H279 R294
Binding residue
(residue number reindexed from 1)		F26 I46 Y106 W138 E148 D168 L169 K170 H231 S235 Y236 N240 H242 R257
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
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1st4, PDBe:1st4, PDBj:1st4
PDBsum1st4
PubMed15068804
UniProtQ96C86|DCPS_HUMAN m7GpppX diphosphatase (Gene Name=DCPS)

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