Structure of PDB 8e05 Chain B Binding Site BS01

Receptor Information
>8e05 Chain B (length=1749) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RSRRTEGIRAAYRRGDRGGARDLLEEACDQCASQLEKGQLLSIPAAYGDL
EMVRYLLSKRLVELPTEPTDDNPAVVAAYFGHTAVVQELLESLPGPCSPQ
RLLNWMLALACQRGHLGVVKLLVLTHGADPESYAVRKNEFPVIVRLPLYA
AIKSGNEDIAIFLLRHGAYFCSYILLDSPDPSKHLLRKYFIEASTALRVK
WSHLRLPWVDLDWLIDISCQITELDLSANCLATLPSVIPWGLINLRKLNL
SDNHLGELPGVQSSDEIICSRLLEIDISSNKLSHLPPGFLHLSKLQKLTA
SKNCLEKLFEEENATNWIGLRKLQELDISDNKLTELPALFLHSFKSLNSL
NVSRNNLKVFPDPWACPLKCCKASRNALECLPDKMAVFWKNHLKDVDFSE
NALKEVPLGLFQLDALMFLRLQGNQLAALPPQEKWTCRQLKTLDLSRNQL
GVLEFPAFLSESLEVLCLNDNHLDTVPPSVCLLKSLSELYLGNNPGLREL
PPELGQLGNLWQLDTEDLTISNVPAEIQKEGPKAMLSYLRAQLRKAEKCK
LMKMIIVGPPRQGKSTLLEILQTGRAPQVVHGEATIRTTKWELQRPAGSR
AKVESVEFNVWDIGGPASMATVNQCFFTDKALYVVVWNLALGEEAVANLQ
FWLLNIEAKAPNAVVLVVGTHLDLIEAKFRVERIATLRAYVLALCRSPSG
SRATGFPDITFKHLHEISCKSLEGQEGLRQLIFHVTCSMKDCQRLAGRLI
PRSYLSLQEAVLAEQQRRSRDDDVQYLTDRQLEQLVEQTPDNDIKDYEDL
QSAISFLIETGTLLHFPDTSHGLRNLYFLDPIWLSECLQRIFNIKGSRSV
AKNGVIRAEDLRMLLVGTGFTQQTEEQYFQFLAKFEIALPVANDSYLLPH
LLPSKPGLDTHGMRHPTANTIQRVFKMSFVPVGFWQRFIARMLISLAEMD
LQLFTIYSFTGNQRNRCSTFRVKRNQTIYWQEGLLVTFDGGYLSVESSDV
NWKKKKSGGMKIVCQSEVRDFSAMAFITDHVNSLIDQWFPALTATESDGT
PLMEQYVPCPVCETAWASEDVQYFDMEDCVLTAIERDFISCPRHPDLPVP
LQELVPELFMTDFPARLFLENSKLEHSEDEGSVLGQGGSGTVIYRARYQG
QPVAVKRFHIKKFADTMLRHLRATDAMKNFSEFRQEASMLHALQHPCIVA
LIGISIHPLCFALELAPLSSLNTVLSENARDSSFIPLGHMLTQKIAYQIA
SGLAYLHKKNIIFCDLKSDNILVWSLDVKEHINIKLSDYGIIVYDEKVDM
FSYGMVLYELLSGQRPALGHHQLQIAKKLSKGIRPVLGQPEEVQFRRLQA
LMMECWDTKPEKRPLALSVVSQMKDPTFATFMYELCCGKQTAFFSSQGQE
YTVVFWDGKEESRNYTVVNTEKGLMEVQRMCCPGMKVSCQLQVQRSLWTA
TEDQKIYIYTLKGMCPLNTPQQALDTPAVVTCFLAVPVIKKNSYLVLAGL
ADGLVAVFPVVRGTPKDSCSYLCSHTANRSKFSIADEDARQNPYPVKAME
VVNSGSEVWYSNGPGLLVIDCASLEICRRLEPYMAPSMVTSVVCSSEGRG
EEVVWCLDDKANSLVMYHSTTYQLCARYFCGVPSPLRDMFPVRPFSQHLQ
AVKILAVRDLIWVPRRGGDVIVIGLEKDSGAQRGRVIAVLKARELTPHGV
LVDAAVVAKDTVVCTFENENTEWCLAVWRGWGAREFDIFYQSYEELGRL
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 chain8e05 Chain B Residue 2101 [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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PDB8e05 Structure of LRRK1
Resolution4.6 Å
Binding residue
(original residue number in PDB)		P647 R648 G650 K651 S652 T653 H758 D760 S805 C806
Binding residue
(residue number reindexed from 1)		P560 R561 G563 K564 S565 T566 H671 D673 S718 C719
Annotation score3
Enzymatic activity
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0005525 GTP binding
GO:0042802 identical protein binding
GO:0044024 histone H2AS1 kinase activity
GO:0046872 metal ion binding
GO:0106310 protein serine kinase activity
Biological Process
GO:0006338 chromatin remodeling
GO:0006468 protein phosphorylation
GO:0009966 regulation of signal transduction
GO:0016310 phosphorylation
GO:0035556 intracellular signal transduction
GO:0036035 osteoclast development
GO:0045453 bone resorption
GO:0050731 positive regulation of peptidyl-tyrosine phosphorylation
GO:0090263 positive regulation of canonical Wnt signaling pathway
GO:1902533 positive regulation of intracellular signal transduction
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol
GO:0005886 plasma membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8e05, PDBe:8e05, PDBj:8e05
PDBsum8e05
PubMed37857821
UniProtQ38SD2|LRRK1_HUMAN Leucine-rich repeat serine/threonine-protein kinase 1 (Gene Name=LRRK1)

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