Structure of PDB 8fo7 Chain C Binding Site BS02

Receptor Information
>8fo7 Chain C (length=1141) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVPYNRMKLMIVGNTGSGKTTLLQQLMKQSATVGIDVKDWPIQIRDKRKR
DLVLNVWDFAGREEFYSTHPHFMTQRALYLAVYDLSKGQAEVDAMKPWLF
NIKARASSSPVILVGTHLDVSDEKQRKACMSKITKELLNKRGFPAIRDYH
FVNATEESDALAKLRKTIINESLNFKIRDQLVVGQLIPDCYVELEKIILS
ERKNVPIEFPVIDRKRLLQLVRENQLQLDENELPHAVHFLNESGVLLHFQ
DPALQLSDLYFVEPKWLCKIMAQILTVKGIISRRDVEKFLSKKRKFPKNY
MTQYFKLIALPIYLLVPSSLSDHRPVIELPHCENSEIIIRLYEMPYFPMG
FWSRLINRLLEISPYMLSGRERALRPNRRYWRQGIYLNWSPEAYCLVGSE
VLDNHPESFLKITVPSCRKGCILLGQVVDHIDSLMEEWFPGLLEITLLKK
WALYSFNDGEEHQKILLDDLMKKAEEGDLLVNPDQPRLTIPISQIAPDLI
LADLPRNIMLNNDELEFEQAPEFLLGDGSFGSVYRAAYEGEEVAVKIFNK
HTSLRLLRQELVVLCHLHHPSLISLLAAGIRPRMLVMELASKGSLDRLLQ
QDKASLTRTLQHRIALHVADGLRYLHSAMIIYRDLKPHNVLLFTLYPNAA
IIAKIADYGIAQYCCRMGIKTSEGTPGFRAPEVARGNVIYNQQADVYSFG
LLLYDILTTGGRIVEGLKFPNEFDELEIQGKLPDPVKEYGCAPWPMVEKL
IKQCLKENPQERPTSAQVFDILNSAELVCLTRRILLPKNVIVECMVATHH
NSRNASIWLGCGHTDRGQLSFLDLNTEGYTSEEVADSRILCLALVHLPVE
KESWIVSGTQSGTLLVINTEDGKKRHTLEKMTDSVTCLYCNSFQKNFLLV
GTADGKLAIFEDKTVKLKGAAPLKILNIGNVSTPLMCLSESTNSTERNVM
WGGCGTKIFSFSNDFTIQKLIETRTSQLFSYAAFSDSNIITVVVDTALYI
AKQNSPVVEVWDKKTEKLCGLIDCVHFLREVTSYSGRVKTLCLQKNTALW
IGTGGGHILLLDLSTRRLIRVIYNFCNSVRVMMTAQLGSLKNVMLVLGYN
REIQSCLTVWDINLPHEVQNLEKHIEVRKELAEKMRRTSVE
Ligand information
Ligand ID4K4
InChIInChI=1S/C31H38N8O3/c1-35-15-17-38(18-16-35)22-11-13-39(14-12-22)29(40)21-9-10-24(27(19-21)42-4)33-31-32-20-26-28(34-31)36(2)25-8-6-5-7-23(25)30(41)37(26)3/h5-10,19-20,22H,11-18H2,1-4H3,(H,32,33,34)
InChIKeyIWMCPJZTADUIFX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CN1CCN(CC1)C2CCN(CC2)C(=O)c3ccc(c(c3)OC)Nc4ncc5c(n4)N(c6ccccc6C(=O)N5C)C
CACTVS 3.385COc1cc(ccc1Nc2ncc3N(C)C(=O)c4ccccc4N(C)c3n2)C(=O)N5CCC(CC5)N6CCN(C)CC6
ACDLabs 12.01c23N(c1c(cccc1)C(=O)N(c2cnc(n3)Nc6c(cc(C(N5CCC(N4CCN(C)CC4)CC5)=O)cc6)OC)C)C
FormulaC31 H38 N8 O3
Name2-[(2-methoxy-4-{[4-(4-methylpiperazin-1-yl)piperidin-1-yl]carbonyl}phenyl)amino]-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one
ChEMBLCHEMBL2012582
DrugBank
ZINCZINC000084605049
PDB chain8fo7 Chain C Residue 2602 [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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PDB8fo7 Pharmacology of LRRK2 with type I and II kinase inhibitors revealed by cryo-EM
Resolution3.52 Å
Binding residue
(original residue number in PDB)		L1884 L1885 A1904 M1947 A1950 G1953 R1957 D2017
Binding residue
(residue number reindexed from 1)		L524 L525 A544 M587 A590 G593 R597 D657
Annotation score1
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:8fo7, PDBe:8fo7, PDBj:8fo7
PDBsum8fo7
PubMed38263358
UniProtQ5S007|LRRK2_HUMAN Leucine-rich repeat serine/threonine-protein kinase 2 (Gene Name=LRRK2)

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