SMTL ID : 8u8a.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x 0LI: 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzam ide(Non-covalent)

0LI.1: 21 residues within 4Å: Chain A: F.1890, V.1893, A.1904, K.1906, E.1920, V.1923, L.1924, L.1927, M.1947, E.1948, L.1949, A.1950, I.1990, I.1991, Y.1992, R.1993, L.2001, I.2015, A.2016, D.2017, Y.2018 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.1893, A:E.1920 Hydrogen bonds: A:E.1920, A:E.1920, A:A.1950, A:D.2017 pi-Stacking: A:F.1890 Halogen bonds: A:I.2015 0LI.3: 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, I.1990, I.1991, Y.1992, R.1993, L.2001, I.2015, A.2016, D.2017, Y.2018 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.1893, B:E.1920 Hydrogen bonds: B:E.1920, B:E.1920, B:A.1950, B:D.2017 pi-Stacking: B:F.1890 Halogen bonds: B:I.2015

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

GDP.2: 11 residues within 4Å: Chain A: G.1344, S.1345, G.1346, K.1347, T.1348, T.1349, T.1368, H.1453, D.1455, N.1489, A.1490 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.1347, A:T.1348, A:T.1349, A:T.1368, 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, A:H.1453 GDP.4: 11 residues within 4Å: Chain B: G.1344, S.1345, G.1346, K.1347, T.1348, T.1349, T.1368, H.1453, D.1455, N.1489, A.1490 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:K.1347, B:T.1348, B:T.1349, 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

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
C

Leucine-rich repeat serine/threonine-protein kinase 2

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