Structure of PDB 5kty Chain A Binding Site BS02

Receptor Information
>5kty Chain A (length=397) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKPACIKALTRIFKISDQDNDGTLNDAELNFFQRICFNTPLAPQALEDVK
NVVRKHISDGVADSGLTLKGFLFLHTLFIETTWTVLRRFGYDDDLDLTPE
YLFPLLKIPPDCTTELNHHAYLFLQSTFDKHDLDRDCALSPDELKDLFKV
FPYIPWGPDVNNTVCTNERGWITYQGFLSQWTLTTYLDVQRCLEYLGYLG
YSILTEQESQASAVTVTRDKKIDLQKKQTQRNVFRCNVIGVKNCGKSGVL
QALLGRNLMRQKKIREDHKSYYAINTVYVYGQEKYLLLHDISESEFLTEA
EIICDVVCLVYDVSNPKSFEYCARIFKQHFMDSRIPCLIVAAKSDLHEVK
QEYSISPTDFCRKHKMPPPQAFTCNTADAPSKDIFVKLTTMAMYPHV
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 chain5kty Chain A Residue 703 [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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PDB5kty Structural insights into Parkin substrate lysine targeting from minimal Miro substrates.
Resolution2.522 Å
Binding residue
(original residue number in PDB)		K427 N428 K431 K454 D475 S477 E478
Binding residue
(residue number reindexed from 1)		K242 N243 K246 K269 D290 S292 E293
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.5.-
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005509 calcium ion binding
GO:0005525 GTP binding

View graph for
Molecular Function
External links
PDB RCSB:5kty, PDBe:5kty, PDBj:5kty
PDBsum5kty
PubMed27605430
UniProtQ8IXI2|MIRO1_HUMAN Mitochondrial Rho GTPase 1 (Gene Name=RHOT1)

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