Structure of PDB 6hh2 Chain A Binding Site BS01

Receptor Information
>6hh2 Chain A (length=174) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RDHLFKVLVVGDAAVGKTSLVQRYSQDSFSKHYKSTVGVDFALKVLQWSD
YEIVRLQLWDIAGLERFTSMTRLYYRDASAAVIMFDVTNATTFSNSQRWK
QDLDSKLTLPNGEPVPALLLANKSDLSPWAVSRDQIDRFSKENGFTGWTE
TSVKENKNINEAMRVLIEKMMRNS
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 chain6hh2 Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6hh2 LRRK2 binds to the Rab32 subfamily in a GTP-dependent mannerviaits armadillo domain.
Resolution1.449 Å
Binding residue
(original residue number in PDB)		A17 G19 K20 T21 S22 N125 K126 D128 L129 S155 V156 K157
Binding residue
(residue number reindexed from 1)		A14 G16 K17 T18 S19 N122 K123 D125 L126 S152 V153 K154
Annotation score4
Binding affinityMOAD: Kd=2.7uM
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:6hh2, PDBe:6hh2, PDBj:6hh2
PDBsum6hh2
PubMed31552791
UniProtO14966|RAB7L_HUMAN Ras-related protein Rab-7L1 (Gene Name=RAB29)

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