Structure of PDB 1ryf Chain A Binding Site BS01

Receptor Information
>1ryf Chain A (length=170) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSMQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDG
KPVNLGLWDTAIADVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIIL
VGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQ
RGLKTVFDEAIRAVLCPPPV
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 chain1ryf Chain A Residue 538 [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]
PDB1ryf Alternative Splicing of Rac1 Generates Rac1b, a Self-activating GTPase
Resolution1.75 Å
Binding residue
(original residue number in PDB)		A13 G15 K16 T17 C18 F28 K135 D137 L138 S177 A178 L179
Binding residue
(residue number reindexed from 1)		A15 G17 K18 T19 C20 F30 K104 D106 L107 S146 A147 L148
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=8.80,Kd=1.6nM
Enzymatic activity
Enzyme Commision number 3.6.5.2: small monomeric GTPase.
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding
Biological Process
GO:0007264 small GTPase-mediated signal transduction

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1ryf, PDBe:1ryf, PDBj:1ryf
PDBsum1ryf
PubMed14625275
UniProtP63000|RAC1_HUMAN Ras-related C3 botulinum toxin substrate 1 (Gene Name=RAC1)

[Back to BioLiP]