SMTL ID : 8u8b.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

GDP.1: 12 residues within 4Å: Chain A: G.1344, S.1345, G.1346, K.1347, T.1348, T.1349, S.1366, T.1368, H.1453, D.1455, N.1489, A.1490 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.1344, A:K.1347, A:T.1348, A:T.1349, A:T.1368, A:T.1368, A:H.1453, A:N.1489, A:A.1490 Salt bridges: A:K.1347, A:D.1455 pi-Cation interactions: A:H.1453 GDP.3: 12 residues within 4Å: Chain B: G.1344, S.1345, G.1346, K.1347, T.1348, T.1349, S.1366, T.1368, H.1453, D.1455, N.1489, A.1490 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.1344, B:K.1347, B:T.1348, B:T.1368, B:T.1368, B:T.1368, B:H.1453, B:N.1489, B:A.1490 Salt bridges: B:K.1347, B:D.1455 pi-Cation interactions: B:H.1453, B:H.1453

2 x 919: 4-[4-({[3-tert-butyl-1-(quinolin-6-yl)-1H-pyrazol-5-yl]carbamoyl}amino)-3-fluorophenoxy]-N-methylpyridine-2-carboxamide(Non-covalent)

919.2: 22 residues within 4Å: Chain A: G.1886, F.1890, V.1893, K.1906, E.1920, V.1923, L.1927, L.1932, L.1945, M.1947, E.1948, L.1949, A.1950, G.1953, L.1985, Y.1992, L.2001, I.2015, A.2016, D.2017, Y.2018, G.2019 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:E.1920, A:V.1923, A:V.1923, A:L.1927, A:L.1932, A:L.1985, A:Y.1992, A:I.2015, A:A.2016, A:Y.2018 Hydrogen bonds: A:E.1920, A:E.1920, A:E.1920, A:A.1950, A:A.1950, A:D.2017 pi-Cation interactions: A:K.1906 919.4: 22 residues within 4Å: Chain B: G.1886, F.1890, V.1893, K.1906, E.1920, V.1923, L.1927, L.1932, L.1945, M.1947, E.1948, L.1949, A.1950, G.1953, L.1985, Y.1992, L.2001, I.2015, A.2016, D.2017, Y.2018, G.2019 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:V.1893, B:E.1920, B:V.1923, B:L.1927, B:L.1932, B:L.1985, B:Y.1992, B:I.2015, B:A.2016, B:Y.2018 Hydrogen bonds: B:E.1920, B:E.1920, B:E.1920, B:A.1950, B:A.1950, B:D.2017 pi-Cation interactions: B:K.1906

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
A

B
B

Leucine-rich repeat serine/threonine-protein kinase 2

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