Structure of PDB 6ff8 Chain B Binding Site BS01

Receptor Information
>6ff8 Chain B (length=170) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ETREHLFKVLVIGELGVGKTSIIKRYVHQLFSQHYRATIGVDFALKVLNW
DSRTLVRLQLWDIAGLERFGNMTRVYYKEAVGAFVVFDISRSSTFEAVLK
WKSDLDSKVHLPNGSPIPAVLLANKCDSPSQVDQFCKEHGFAGWFETSAK
DNINIEEAARFLVEKILVNH
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 chain6ff8 Chain B Residue 900 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6ff8 LRRK2 binds to the Rab32 subfamily in a GTP-dependent mannerviaits armadillo domain.
Resolution2.13 Å
Binding residue
(original residue number in PDB)		G35 G37 K38 T39 S40 F50 Q52 Y54 T57 N143 K144 D146 S174 A175 K176
Binding residue
(residue number reindexed from 1)		G16 G18 K19 T20 S21 F31 Q33 Y35 T38 N124 K125 D127 S148 A149 K150
Annotation score4
Binding affinityMOAD: Kd=1.2uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding
Biological Process
GO:0016192 vesicle-mediated transport
Cellular Component
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0031982 vesicle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6ff8, PDBe:6ff8, PDBj:6ff8
PDBsum6ff8
PubMed31552791
UniProtQ13637|RAB32_HUMAN Ras-related protein Rab-32 (Gene Name=RAB32)

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