Structure of PDB 5osy Chain A Binding Site BS01

Receptor Information
>5osy 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]
SAPVRLPFSGFRLQKVLRESARDKIIFLHGKVNEASGDGDGEDAVVILEK
TPFQVEQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLNDVKTTVVYPAT
EKHLQKYLRQDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEA
DRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPE
HLPLLRNILHQGQEAILQRYRMKGDHLRVYLHYLPSYYHLHVHFTALGFE
APGSGVERAHLLAEVIENLECDPRHYQQRTLTFALRADDPLLKLLQEAQQ
Ligand information
Ligand IDAJQ
InChIInChI=1S/C21H29N10O15P3S3/c1-29-5-31(15-9(29)17(37)28-21(23)26-15)19-13(35)11(33)7(44-19)3-52-48(40,41)46-49(42,50)45-47(38,39)51-2-6-10(32)12(34)18(43-6)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-,22,23,25,26,27,28,36,37,38,39,40,41,42,50)/p+1/t6-,7-,10-,11-,12-,13-,18-,19-,49-/m1/s1
InChIKeyUOUACWJATBZTPY-ACTLBPNMSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C[n+]1cn(c2c1C(=O)NC(=N2)N)C3C(C(C(O3)CSP(=O)(O)OP(=O)(OP(=O)(O)SCC4C(C(C(O4)n5cnc6c5NC(=NC6=O)N)O)O)S)O)O
OpenEye OEToolkits 2.0.6C[n+]1cn(c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)CSP(=O)(O)O[P@@](=O)(OP(=O)(O)SC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5NC(=NC6=O)N)O)O)S)O)O
CACTVS 3.385C[n+]1cn([C@@H]2O[C@H](CS[P](O)(=O)O[P@@](S)(=O)O[P](O)(=O)SC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5C(=O)N=C(N)Nc45)[C@@H](O)[C@H]2O)c6N=C(N)NC(=O)c16
CACTVS 3.385C[n+]1cn([CH]2O[CH](CS[P](O)(=O)O[P](S)(=O)O[P](O)(=O)SC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5C(=O)N=C(N)Nc45)[CH](O)[CH]2O)c6N=C(N)NC(=O)c16
FormulaC21 H30 N10 O15 P3 S3
Name[(2~{S},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl-[[[(2~{S},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl]oxy-phosphinic acid
ChEMBL
DrugBank
ZINC
PDB chain5osy Chain A Residue 400 [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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PDB5osy 5'-Phosphorothiolate Dinucleotide Cap Analogues: Reagents for Messenger RNA Modification and Potent Small-Molecular Inhibitors of Decapping Enzymes.
Resolution2.06 Å
Binding residue
(original residue number in PDB)		R54 D59 I61 E85 K142 Y143 W175 E185 D205 L206 K207 Y217 H268 S272 Y273 P288 R294
Binding residue
(residue number reindexed from 1)		R18 D23 I25 E49 K106 Y107 W139 E149 D169 L170 K171 Y181 H232 S236 Y237 P252 R258
Annotation score2
Binding affinityMOAD: ic50=0.0447uM
PDBbind-CN: -logKd/Ki=7.37,IC50=0.0430uM
Enzymatic activity
Enzyme Commision number 3.6.1.59: 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase.
Gene Ontology
Molecular Function
GO:0016787 hydrolase activity
Biological Process
GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5osy, PDBe:5osy, PDBj:5osy
PDBsum5osy
PubMed29676910
UniProtQ96C86|DCPS_HUMAN m7GpppX diphosphatase (Gene Name=DCPS)

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