Structure of PDB 6am0 Chain E Binding Site BS02

Receptor Information
>6am0 Chain E (length=257) Species: 284590 (Kluyveromyces lactis NRRL Y-1140) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLPLLRPFETVSLENAVEDLVVRFILNVPPEDLSTVERVLFHFEEASWFY
TDFVKLMNPYLPNLSIKSFSKIVIDICPLIWNWDITPENALVKFSNYKKT
IPVRGAAIFNDSLSKILLLRGINSKHWSFPRGKIGKDEDDVACCIREVKE
QTGFDLTGFIDADQYVERNMNGKNFKIFLVKGVPEDFEFKPEHKNEIQAI
EWKDFKKLSKAITKNVFLVNSMIRPLSLYVKNEKRAKDENKLKLYAEEHL
KSILGLN
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 chain6am0 Chain E Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6am0 Structure of the activated Edc1-Dcp1-Dcp2-Edc3 mRNA decapping complex with substrate analog poised for catalysis.
Resolution2.84 Å
Binding residue
(original residue number in PDB)
W49 D53 K100 H127 R132 K134 K174 F176 E197 F223
Binding residue
(residue number reindexed from 1)
W48 D52 K99 H126 R131 K133 K173 F175 E196 F217
Annotation score3
Enzymatic activity
Enzyme Commision number ?
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:6am0, PDBe:6am0, PDBj:6am0
PDBsum6am0
PubMed29559651
UniProtQ6CIU1

[Back to BioLiP]