SMTL ID : 8u7l.1

Cryo-EM structure of LRRK2 bound to type II inhibitor GZD824

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

GDP.1: 10 residues within 4Å: Chain A: G.1344, S.1345, G.1346, K.1347, T.1348, T.1349, T.1368, H.1453, N.1489, A.1490 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.1344, A:K.1347, A:T.1348, A:T.1368, A:T.1368, A:H.1453, A:D.1455, A:A.1490 Salt bridges: A:K.1347 pi-Cation interactions: A:H.1453, A:H.1453 GDP.3: 10 residues within 4Å: Chain B: S.1345, G.1346, K.1347, T.1348, T.1349, S.1366, T.1368, H.1453, N.1489, A.1490 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.1344, B:K.1347, B:T.1348, B:T.1368, B:T.1368, B:H.1453, B:D.1455, B:A.1490 Salt bridges: B:K.1347 pi-Cation interactions: B:H.1453, B:H.1453

2 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: 19 residues within 4Å: Chain A: F.1890, V.1893, A.1904, K.1906, E.1920, L.1924, L.1927, M.1947, E.1948, L.1949, A.1950, I.1990, I.1991, Y.1992, L.2001, I.2015, A.2016, D.2017, Y.2018 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.1893, A:A.1904, A:K.1906, A:L.1924, A:L.2001, A:D.2017 Hydrogen bonds: A:E.1920, A:A.1950, A:A.1950, A:D.2017 Halogen bonds: A:I.2015 T3X.4: 21 residues within 4Å: Chain B: F.1890, V.1893, A.1904, K.1906, E.1920, V.1923, L.1924, L.1927, M.1947, E.1948, L.1949, A.1950, G.1953, I.1990, I.1991, Y.1992, L.2001, I.2015, A.2016, D.2017, Y.2018 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.1893, B:A.1904, B:K.1906, B:L.1924, B:L.2001, B:D.2017 Hydrogen bonds: B:E.1920, B:A.1950, B:A.1950, B:D.2017

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

2024-01-31

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Leucine-rich repeat serine/threonine-protein kinase 2

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