Structure of PDB 5osy Chain B Binding Site BS01

Receptor Information
>5osy Chain B (length=291) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VRLPFSGFRLQKVLRESARDKIIFLHGKVNEGEDAVVILEKTPFQVEQVA
QLLTGSPELQLQFSNDIYSTYHLFPPRQLNDVKTTVVYPATEKHLQKYLR
QDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPD
PSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNIL
HQGQEAILQRYRMKGDHLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERA
HLLAEVIENLECDPRHYQQRTLTFALRADDPLLKLLQEAQQ
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 B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)
W175 E185 L206
Binding residue
(residue number reindexed from 1)
W130 E140 L161
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

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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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