SMTL ID : 8tzf.1

Structure of full length LRRK2 bound to GZD-824 (I2020T mutant)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

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

GDP.1: 14 residues within 4Å: Chain A: N.1342, G.1344, G.1346, K.1347, T.1348, T.1349, Q.1365, T.1368, G.1397, T.1452, H.1453, D.1455, N.1489, A.1490 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.1344, A:G.1346, A:K.1347, A:T.1348, A:T.1348, A:T.1348, A:D.1394, A:G.1397, A:A.1490 Salt bridges: A:K.1347, A:D.1455 pi-Cation interactions: A:H.1453, A:H.1453

1 x T3X: 4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}-3-[(1H-pyrazolo[3,4-b]pyridin-5-yl)ethynyl]benzamide(Non-covalent)

T3X.2: 22 residues within 4Å: Chain A: L.1885, F.1890, A.1904, K.1906, E.1920, L.1924, L.1927, L.1932, M.1947, E.1948, L.1949, A.1950, G.1953, I.1990, I.1991, Y.1992, R.1993, L.2001, I.2015, A.2016, D.2017, Y.2018 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.1885, A:K.1906, A:L.1924, A:M.1947, A:L.2001, A:L.2001, A:Y.2018, A:Y.2018 Hydrogen bonds: A:A.1950, A:A.1950, A:D.2017 Salt bridges: A:D.2017, A:D.2017 pi-Stacking: A:F.1890, A:F.1890 Halogen bonds: A:I.2015

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sanz Murillo, M. et al., Inhibition of Parkinson's disease-related LRRK2 by type I and type II kinase inhibitors: Activity and structures. Sci Adv (2023)

Release Date

2023-12-06

Peptides

Leucine-rich repeat serine/threonine-protein kinase 2: A
designed ankyrin repeat proteins E11: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Leucine-rich repeat serine/threonine-protein kinase 2

designed ankyrin repeat proteins E11

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