Structure of PDB 5kq4 Chain B Binding Site BS01

Receptor Information
>5kq4 Chain B (length=242) Species: 284812 (Schizosaccharomyces pombe 972h-) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GGSMSFTNATFSQVLDDLSARFILNLPAEEQSSVERLCFQIEQAHWFYED
FIRAQNDQLPSLGLRVFSAKLFAHCPLLWKWSKVHEEAFDDFLRYKTRIP
VRGAIMLDMSMQQCVLVKGWKASSGWGFPKGKIDKDESDVDCAIREVYEE
TGFDCSSRINPNEFIDMTIRGQNVRLYIIPGISLDTRFESRTRKEISKIE
WHNLMDLPTFKKNKPQTMKNKFYMVIPFLAPLKKWIKKRNIA
Ligand information
Ligand ID6VQ
InChIInChI=1S/C22H32N10O19P4S2/c1-29-5-31(15-9(29)17(37)27-21(23)25-15)19-13(35)11(33)7(47-19)3-45-54(43,56)50-52(39,40)49-53(41,42)51-55(44,57)46-4-8-12(34)14(36)20(48-8)32-6-30(2)10-16(32)26-22(24)28-18(10)38/h5-8,11-14,19-20,33-36H,3-4H2,1-2H3,(H8-2,23,24,25,26,27,28,37,38,39,40,41,42,43,44,56,57)/p+2/t7-,8-,11-,12-,13-,14-,19-,20-,54-,55-/m1/s1
InChIKeySZQMTBAJCPCVLP-BZDQESSTSA-P
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5C[n+]1cn(c2c1C(=O)N=C(N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(OP(=O)(O)OP(=O)(O)O[P@@](=O)(OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5c[n+](c6c5NC(=NC6=O)N)C)O)O)S)S)O)O
CACTVS 3.385C[n+]1cn([C@@H]2O[C@H](CO[P@](S)(=O)O[P](O)(=O)O[P](O)(=O)O[P@@](S)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4c[n+](C)c5C(=O)N=C(N)Nc45)[C@@H](O)[C@H]2O)c6NC(=NC(=O)c16)N
OpenEye OEToolkits 2.0.5C[n+]1cn(c2c1C(=O)N=C(N2)N)C3C(C(C(O3)COP(=O)(OP(=O)(O)OP(=O)(O)OP(=O)(OCC4C(C(C(O4)n5c[n+](c6c5NC(=NC6=O)N)C)O)O)S)S)O)O
CACTVS 3.385C[n+]1cn([CH]2O[CH](CO[P](S)(=O)O[P](O)(=O)O[P](O)(=O)O[P](S)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4c[n+](C)c5C(=O)N=C(N)Nc45)[CH](O)[CH]2O)c6NC(=NC(=O)c16)N
FormulaC22 H34 N10 O19 P4 S2
Name[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-3~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] [[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-3~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl]oxy-oxidanyl-phosphoryl] hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain5kq4 Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5kq4 Structural basis of mRNA-cap recognition by Dcp1-Dcp2.
Resolution2.56 Å
Binding residue
(original residue number in PDB)
W43 D47 D88 Y92 K93 R95 K127 R167 Y220
Binding residue
(residue number reindexed from 1)
W46 D50 D91 Y95 K96 R98 K130 R170 Y223
Annotation score3
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:5kq4, PDBe:5kq4, PDBj:5kq4
PDBsum5kq4
PubMed27694842
UniProtO13828|DCP2_SCHPO mRNA decapping complex subunit 2 (Gene Name=dcp2)

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