Structure of PDB 4lhv Chain A Binding Site BS01

Receptor Information
>4lhv Chain A (length=165) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSHDYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIEL
DGKRIKLQIWDTTTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHAS
ADVEKMILGNKCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENA
FFTLARDIKAKMDKK
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 chain4lhv Chain A Residue 201 [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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PDB4lhv Intermediates in the Guanine Nucleotide Exchange Reaction of Rab8 Protein Catalyzed by Guanine Nucleotide Exchange Factors Rabin8 and GRAB.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		G18 V19 G20 K21 T22 C23 F33 N34 N121 K122 D124 S151 A152 K153
Binding residue
(residue number reindexed from 1)		G16 V17 G18 K19 T20 C21 F31 N32 N110 K111 D113 S140 A141 K142
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=10.00,Kd=0.1nM
Enzymatic activity
Enzyme Commision number 3.6.5.2: small monomeric GTPase.
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding

View graph for
Molecular Function
External links
PDB RCSB:4lhv, PDBe:4lhv, PDBj:4lhv
PDBsum4lhv
PubMed24072714
UniProtP61006|RAB8A_HUMAN Ras-related protein Rab-8A (Gene Name=RAB8A)

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