Structure of PDB 8i0p Chain C Binding Site BS01

Receptor Information
>8i0p Chain C (length=896) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EVVLHEDKKYYPTAEEVYGPEVETIVQEEDTQPLTEPIIKFTLMEQTLPV
TVYEMDFLADLMDNSELIRNVTLCGHLHHGKTCFVDCLIEQTHPEIRKRY
DQDLCYTDILFTEQERGVGIKSTPVTVVLPDTKGKSYLFNIMDTPGHVNF
SDEVTAGLRISDGVVLFIDAAEGVMLNTERLIKHAVQERLAVTVCINKID
RLILELKLPPTDAYYKLRHIVDEVNGLISMYSTDENLILSPLLGNVCFSS
SQYSICFTLGSFAKIYADTFGDINYQEFAKRLWGDIYFNPKTRKFTKKAP
TSSSQRSFVEFILEPLYKILAQVVGDVDTSLPRTLDELGIHLTKEELKLN
IRPLLRLVCKKFFGEFTGFVDMCVQHIPSPKVGAKPKIEHTYTGGVDSDL
GEAMSDCDPDGPLMCHTTKMYSTDDGVQFHAFGRVLSGTIHAGQPVKVLG
ENYTLEDEEDSQICTVGRLWISVARYHIEVNRVPAGNWVLIEGVDQPIVK
TATITEPRGNEEAQIFRPLKFNTTSVIKIAVEPVNPSELPKMLDGLRKVN
KSYPSLTTKVEESGEHVILGTGELYLDCVMHDLRKMYSEIDIKVADPVVT
FCETVVETSSLKCFAETPNKKNKITMIAEPLEKGLAEDIENEVVQITWNR
KKLGEFFQTKYDWDLLAARSIWAFGPDATGPNILVDDTLPSEVDKALLGS
VKDSIVQGFQWGTREGPLCDELIRNVKFKILDAVVAQEPLHRGGGQIIPT
ARRVVYSAFLMATPRLMEPYYFVEVQAPADCVSAVYTVLARRRGHVTQDA
PIPGSPLYTIKAFIPAIDSFGFETDLRTHTQGQAFSLSVFHHWQIVPGDP
LDKSIVIRPLEPQPAPHLAREFMIKTRRRKGLSEDVSISKFFDDPM
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain8i0p Chain C Residue 1500 [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]
PDB8i0p Molecular Basis for the activation of Human spliceosome
Resolution3.4 Å
Binding residue
(original residue number in PDB)		H139 H140 G141 K142 C144 G180 P206 G207 K259 D261 S311 S312 Q313
Binding residue
(residue number reindexed from 1)		H78 H79 G80 K81 C83 G119 P145 G146 K198 D200 S250 S251 Q252
Annotation score4
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0030623 U5 snRNA binding
Biological Process
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0042220 response to cocaine
GO:0071466 cellular response to xenobiotic stimulus
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005829 cytosol
GO:0015030 Cajal body
GO:0016020 membrane
GO:0016607 nuclear speck
GO:0043231 intracellular membrane-bounded organelle
GO:0046540 U4/U6 x U5 tri-snRNP complex
GO:0071005 U2-type precatalytic spliceosome
GO:0071007 U2-type catalytic step 2 spliceosome
GO:0071013 catalytic step 2 spliceosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8i0p, PDBe:8i0p, PDBj:8i0p
PDBsum8i0p
PubMed39068178
UniProtQ15029|U5S1_HUMAN 116 kDa U5 small nuclear ribonucleoprotein component (Gene Name=EFTUD2)

[Back to BioLiP]