Structure of PDB 5kq4 Chain E Binding Site BS01

Receptor Information
>5kq4 Chain E (length=235) Species: 284812 (Schizosaccharomyces pombe 972h-) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMSFTNATFSQVLDDLSARFILNLPAEEQSSVERLCFQIEQAHWFYEDFI
RAQNDQLPSLGLRVFSAKLFAHCPLLWKWSKVHEEAFDDFLRYKTRIPVR
GAIMLDMSMQQCVLVKGWKASSGWGFPKGKIDKDESDVDCAIREVYEETG
FDCSSRINPNEFIDMTIRGQNVRLYIIPGISLDTRFESRTEISKIEWHNL
MDLPTFKKNKPNKFYMVIPFLAPLKKWIKKRNIAN
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 E 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)
W117 S121 G122 Y220
Binding residue
(residue number reindexed from 1)
W118 S122 G123 Y215
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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