Structure of PDB 4yzm Chain A Binding Site BS01

Receptor Information
>4yzm Chain A (length=260) Species: 44689 (Dictyostelium discoideum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RLPTLADNEIEYEKQIGKGGFGLVHKGRLVKDKSVVAIKSLILTEMIEKF
QEFQREVFIMSNLNHPNIVKLYGLMHNPPRMVMELVPCGDLYHRLLDKAH
PIKWSVKLRLMLDIALGIEYMQNQNPPIVHRDLRSPNILLQSLDENAPVC
AKVADFGLSQQLGNFQWMAPETIGAEEYTEKADTYSFAMILYTILTGEGP
FDEYSYGKIKFINMIREEGLRPTIPEDCPPRLRNVIELCWSGDPKKRPHF
SYIVKELSEL
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 chain4yzm Chain A Residue 1301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4yzm Structural Characterization of LRRK2 Inhibitors.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		I1032 G1035 K1055 M1105 E1106 L1107 V1108 P1109 G1111 L1161
Binding residue
(residue number reindexed from 1)		I16 G19 K39 M83 E84 L85 V86 P87 G89 L139
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.27,IC50=5.38uM
Enzymatic activity
Catalytic site (original residue number in PDB) D1154 R1156 P1158 N1159 D1177 N1194
Catalytic site (residue number reindexed from 1) D132 R134 P136 N137 D155 N164
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004713 protein tyrosine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4yzm, PDBe:4yzm, PDBj:4yzm
PDBsum4yzm
PubMed25897865
UniProtQ6XHB2|ROCO4_DICDI Probable serine/threonine-protein kinase roco4 (Gene Name=roco4)

[Back to BioLiP]