Structure of PDB 8fo7 Chain C Binding Site BS01

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 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 chain8fo7 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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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)		S1345 G1346 T1348 T1349 T1368 T1452 H1453 A1490
Binding residue
(residue number reindexed from 1)		S17 G18 T20 T21 T32 T116 H117 A154
Annotation score4
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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