Structure of PDB 8u7h Chain C Binding Site BS01

Receptor Information
>8u7h Chain C (length=1111) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVPYNRMKLMIVGNTGSGKTTLLQQLMKMQSATVGIDVKDWPIQIRDKRK
RDLVLNVWDFAGREEFYSTHPHFMTQRALYLAVYDLSKGQAEVDAMKPWL
FNIKARASSSPVILVGTHLDVSDEKQRKACMSKITGFPAIRDYHFVNATE
ESDALAKLRKTIINESLNFKIRDQLVVGQLIPDCYVELEKIILSERKNVP
IEFPVIDRKRLLQLVRENQLQLDENELPHAVHFLNESGVLLHFQDPALQL
SDLYFVEPKWLCKIMAQILTVHPKGIISRRDVEKFLSKKRKFPKNYMTQY
FKLEYLLVPSSLSDHRPVIELPHCENSEIIIRLYEMPYFPMGFWSRLINR
LLEISPPNRRYWRQGIYLNWSPEAYCLVGSEVLDNHPESFLKITVPSCRK
GCILLGQVVDHIDSLMEEWFPGLLTLLKKWALYSFNDGEEHQKILLDDLM
KKAEEGDLLVNPDQPRLTIPISQIAPDLILADLPRNIMLNNDELEFEQAP
EFLLGDGSFGSVYRAAYEGEEVAVKIFNKHTSLRLLRQELVVLCHLHHPS
LISLLAAGIRPRMLVMELASKGSLDRLLQQDKASLTRTLQHRIALHVADG
LRYLHSAMIIYRDLKPHNVLLFTLYPNAAIIAKIADYGIAQYCCRMGIKT
SEGTPGFRAPEVARGNVIYNQQADVYSFGLLLYDILTTGGRIVEGLKFPN
EFDELEIQGKLPDPVKEYGCAPWPMVEKLIKQCLKENPQERPTSAQVFDI
LNSAELVCLTRRILLPKNVIVECMVATHHNSRNASIWLGCGHTDRGQLSF
LDLNTEGYTSEEVADSRILCLALVHLPVEKESWIVSGTQSGTLLVINTED
GKKRHTLEKMTDSVTCLYCQKNFLLVGTADGKLAIFEDKTVKLKGAAPLK
ILNIGNVSTPLMCLSESTNSTERNVMWGGCGTKIFSFSNDFTIQKLIETR
TAFSDSNIITVVVDTALYIAKQNSPVVEVWDKKTEKLCGLIDCVHFLREV
TSYSGRVKTLCLQKNTALWIGTGGGHILLLDLSTRRLIRVIYNFCNSVRV
MMTAQLGSLKNVMLVLGYNRKEIQSCLTVWDINLPHEVQNLEKHIEVRKE
LAEKMRRTSVE
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 chain8u7h Chain C Residue 2601 [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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PDB8u7h Pharmacology of LRRK2 with type I and II kinase inhibitors revealed by cryo-EM.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		G1346 K1347 T1348 T1349 Q1365 A1367 T1368 H1453
Binding residue
(residue number reindexed from 1)		G18 K19 T20 T21 Q30 A32 T33 H118
Annotation score3
Enzymatic activity
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
3.6.5.-
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0005524 ATP binding
GO:0005525 GTP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8u7h, PDBe:8u7h, PDBj:8u7h
PDBsum8u7h
PubMed38263358
UniProtQ5S007|LRRK2_HUMAN Leucine-rich repeat serine/threonine-protein kinase 2 (Gene Name=LRRK2)

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