Structure of PDB 6stf Chain B Binding Site BS01

Receptor Information
>6stf Chain B (length=167) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDG
KRIKLQIWDTATITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHA
SADVEKMILGNKCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVEN
AFFTLARDIKAKMDKKH
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 chain6stf Chain B Residue 901 [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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PDB6stf PINK1-dependent phosphorylation of Serine111 within the SF3 motif of Rab GTPases impairs effector interactions and LRRK2-mediated phosphorylation at Threonine72.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		G18 G20 K21 T22 C23 F33 N34 K122 D124 S151 A152 K153
Binding residue
(residue number reindexed from 1)		G14 G16 K17 T18 C19 F29 N30 K112 D114 S141 A142 K143
Annotation score4
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:6stf, PDBe:6stf, PDBj:6stf
PDBsum6stf
PubMed32227113
UniProtP61006|RAB8A_HUMAN Ras-related protein Rab-8A (Gene Name=RAB8A)

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