Structure of PDB 6hdu Chain A Binding Site BS01

Receptor Information
>6hdu Chain A (length=172) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMQAPHKEHLYKLLVIGDLGVGKTSIIKRYVHQNFSSHYRATIGVDFALK
VLHWDPETVVRLQLWDIAGLERFGNMTRVYYREAMGAFIVFDVTRPATFE
AVAKWKNDLDSKLSLPNGKPVSVVLLANKCDQKMDQFCKEHGFVGWFETS
AKENINIDEASRCLVKHILANE
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 chain6hdu Chain A Residue 900 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6hdu LRRK2 binds to the Rab32 subfamily in a GTP-dependent mannerviaits armadillo domain.
Resolution1.793 Å
Binding residue
(original residue number in PDB)		L18 G19 G21 K22 T23 S24 F34 S36 Y38 A40 T41 G68 N127 K128 D130 S159 A160 K161
Binding residue
(residue number reindexed from 1)		L19 G20 G22 K23 T24 S25 F35 S37 Y39 A41 T42 G69 N128 K129 D131 S150 A151 K152
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:6hdu, PDBe:6hdu, PDBj:6hdu
PDBsum6hdu
PubMed31552791
UniProtP57729|RAB38_HUMAN Ras-related protein Rab-38 (Gene Name=RAB38)

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