Structure of PDB 6vno Chain A Binding Site BS01

Receptor Information
>6vno Chain A (length=1084) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPYNRMKLMIVGNTGSGKTTLLQQLMGIDVKDWPILVLNVWDFAGREEFY
STHPRALYLAVYDLSKGQAEVDAMKPWLFNIKARASSSPVILVGTHLDVS
DEKQRKACMSKITKELLNKRGFPAIRDYHFVNATEESDALAKLRKTIINE
SLNFKIRDQLVVGQLIPDCYVELEKIILSERKNVPIEFPVIDRKRLLQLV
RENQLQLDENELPHAVHFLNESGVLLHFQALQLSDLYFVEPKWLCKIMAQ
ILTVGIISRRDVEKFLSKKRKFPKNYMSQYFKLLEKFQIALPIGEEYLLV
PSSLSDHRPVIELPHCENSEIIIRLYEMPYFPMGFWSRLINRLLEISPYM
LLRPNRMYWRQGIYLNWSPEAYCLVGSEVLDNHPESFLKITVPSCRKGCI
LLGQVVDHIDSLMEEWFPGLLLLKKWALYSFNDGEEHQKILLDDLMKKAE
EGDLLVNPDQPRLTIPISQIAPDLILADLPRNIMLNNDELEFEQAPEFLL
GDGSFGSVYRAAYEGEEVAVKIFNKHTSLRLLRQELVVLCHLHHPSLISL
LAAGIRPRMLVMELASKGSLDRLLQQDKASLTRTLQHRIALHVADGLRYL
HSAMIIYRDLKPHNVLLFTLYPNAAIIAKIADYGPGFRAPEVARGNVIYN
QQADVYSFGLLLYDILTTGGRIVEGLKFPNEFDELEIQGKLPDPVKEYGC
APWPMVEKLIKQCLKENPQERPTSAQVFDILNSAELVCLTRRILLPKNVI
VECMVATHHASIWLGCGHTDRGQLSFLDLNTEGYTSEEVADSRILCLALV
HLPVEKESWIVSGTQSGTLLVINTEDGKKRHTLEKMTDSVTCLYCNFLLV
GTADGKLAIFEDKTVKLKGAAPLKILNIGNVSTPLMCLSESNVMWGGCGT
KIFSFSNDFTIQKLIETRTSQLFSYAAFSDSNIITVVVDTALYIAKQNSP
VVEVWDKKTEKLCGLIDCVHFLREVMMSYSGRVKTLCLQKNTALWIGTGG
GHILLLDLSTRRLIRVIYNFCNSVRVMMTAQLGSLKNVMLVLGYNREIQS
CLTVWDINLPHEVQNLEKHIEVRKELAEKMRRTS
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 chain6vno Chain A 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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PDB6vno Structure of LRRK2 in Parkinson's disease and model for microtubule interaction.
Resolution3.5 Å
Binding residue
(original residue number in PDB)		G1344 S1345 G1346 K1347 T1348 T1349 H1453 D1455 N1489 A1490 T1491
Binding residue
(residue number reindexed from 1)		G15 S16 G17 K18 T19 T20 H96 D98 N132 A133 T134
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D1994 H1998 N1999 D2017
Catalytic site (residue number reindexed from 1) D609 H613 N614 D632
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:6vno, PDBe:6vno, PDBj:6vno
PDBsum6vno
PubMed32814344
UniProtQ5S007|LRRK2_HUMAN Leucine-rich repeat serine/threonine-protein kinase 2 (Gene Name=LRRK2)

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