SMTL ID : 8fo7.1

Cryo-EM structure of LRRK2 bound to type I inhibitor LRRK2-IN-1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 13 residues within 4Å: Chain A: T.17, G.18, S.19, G.20, K.21, T.22, T.23, Q.39, A.41, T.42, T.126, H.127, A.164 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.18, A:G.20, A:K.21, A:T.22, A:T.23, A:Q.39, A:T.42, A:T.42, A:T.126, A:T.126, A:T.126 pi-Stacking: A:H.127 pi-Cation interactions: A:H.127

1 x 4K4: 2-[(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(Non-covalent)

4K4.2: 18 residues within 4Å: Chain A: E.556, L.558, L.559, V.567, R.569, A.578, M.621, E.622, L.623, A.624, S.625, G.627, R.631, H.672, N.673, L.675, A.690, D.691 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.559, A:A.690, A:D.691 Hydrogen bonds: A:A.624, A:A.624

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, H. et al., Pharmacology of LRRK2 with type I and II kinase inhibitors revealed by cryo-EM. Cell Discov (2024)

Release Date

2024-01-17

Peptides

Leucine-rich repeat serine/threonine-protein kinase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Leucine-rich repeat serine/threonine-protein kinase 2