Structure of PDB 5nkk Chain F Binding Site BS01

Receptor Information
>5nkk Chain F (length=253) Species: 6239 (Caenorhabditis elegans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKESVRFLTDFGEISDAISDLLTSSPNFNVISAIGPQGAGKSTLLSMLAG
NNSRQMYREYVFRPVSTIQIDIYIVNHQIFLDCDDSTAMSDTLRLTAFLL
YVSHTVLVVSETHYDKVIIDTLRVAEQIRPYLAIFRPKLAIDRKTNLVFI
KTKASSIDLAPTVIREREELLRLSFQDSRWLKVSQEPFKTLIVLEEFDEQ
IAELREELQKNREDFTVETAAMDEKKWLDMCREVIRDKTLHKTLKEYQRA
MTD
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain5nkk Chain F Residue 401 [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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PDB5nkk Structure of a SMG8-SMG9 complex identifies a G-domain heterodimer in the NMD effector proteins.
Resolution2.64 Å
Binding residue
(original residue number in PDB)		Q95 G98 K99 S100 T101 P122 K241 E284
Binding residue
(residue number reindexed from 1)		Q37 G40 K41 S42 T43 P64 K153 E196
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=5.00,Kd=10uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Biological Process
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

View graph for
Biological Process
External links
PDB RCSB:5nkk, PDBe:5nkk, PDBj:5nkk
PDBsum5nkk
PubMed28389433
UniProtQ9XWJ1|SMG9_CAEEL Nonsense-mediated mRNA decay factor SMG9 (Gene Name=smg-9)

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