SMTL ID : 9c76.1

LRRK2 Roc domain RP (Ras-pocket) complexed to Divarasib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

GDP.1: 19 residues within 4Å: Chain A: A.15, C.16, G.17, S.18, G.19, K.20, T.21, T.22, T.125, H.126, L.127, D.128, V.129, V.161, N.162, A.163, T.164 Ligands: MG.5, 01.7 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:A.15, A:G.17, A:S.18, A:G.19, A:K.20, A:T.21, A:T.21, A:T.22, A:T.22, A:H.126, A:H.126, A:A.163 Salt bridges: A:K.20, A:D.128 pi-Stacking: A:H.126, A:H.126 GDP.8: 18 residues within 4Å: Chain B: A.15, C.16, G.17, S.18, G.19, K.20, T.21, T.22, T.125, H.126, L.127, D.128, V.129, N.162, A.163, T.164 Ligands: MG.10, 01.11 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:A.15, B:G.17, B:S.18, B:G.19, B:K.20, B:T.21, B:T.22, B:T.22, B:H.126, B:N.162, B:A.163 Water bridges: B:K.20, B:K.20, B:K.20, B:T.21, B:T.21, B:T.21 Salt bridges: B:K.20, B:D.128 pi-Stacking: B:H.126, B:H.126

3 x BR: BROMIDE ION(Non-covalent)

BR.2: 5 residues within 4Å: Chain A: H.80, M.82, T.83 Chain B: R.114 Ligands: 01.11 Ligand excluded by PLIP BR.3: 6 residues within 4Å: Chain A: W.49, I.51 Chain B: M.28, K.29, T.30, R.174 Ligand excluded by PLIP BR.4: 6 residues within 4Å: Chain A: R.114 Chain B: P.79, H.80, M.82, T.83 Ligands: 01.7 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: T.21 Ligands: GDP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.21, H2O.1 MG.10: 3 residues within 4Å: Chain B: K.20, T.21 Ligands: GDP.8 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.21, H2O.1, H2O.3, H2O.3, H2O.3

1 x F: FLUORIDE ION(Non-covalent)

F.6: 3 residues within 4Å: Chain A: R.7, H.80, K.185 No protein-ligand interaction detected (PLIP)

2 x 01: 1-{(3S)-4-[(7M)-7-[6-amino-4-methyl-3-(trifluoromethyl)pyridin-2-yl]-6-chloro-8-fluoro-2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}quinazolin-4-yl]-3-methylpiperazin-1-yl}propan-1-one

01.7: 27 residues within 4Å: Chain A: M.11, V.13, G.14, A.15, C.16, G.17, K.20, Y.88, H.106, Y.107, Q.110, I.111, R.114 Chain B: F.68, A.69, G.70, R.71, E.72, Y.75, S.76, H.78, P.79, H.80, F.81, M.82 Ligands: GDP.1, BR.4 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:H.106, A:Y.107, A:Y.107, A:Y.107, A:Q.110, B:Y.75 Hydrogen bonds: A:K.20, B:E.72, B:H.78 01.11: 26 residues within 4Å: Chain A: F.68, A.69, G.70, E.72, E.73, Y.75, S.76, P.79, H.80, F.81, M.82 Chain B: M.11, V.13, G.14, A.15, C.16, G.17, K.20, Y.88, H.106, Y.107, Q.110, I.111, R.114 Ligands: BR.2, GDP.8 16 PLIP interactions: 6 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:Y.75, A:Y.75, B:Y.88, B:Y.107, B:Q.110, B:I.111 Hydrogen bonds: A:P.79, A:M.82, B:K.20 Salt bridges: A:E.72 pi-Cation interactions: A:Y.75 Water bridges: B:Q.110, B:Q.110, B:Q.110 Halogen bonds: B:Y.107, B:Q.110

1 x IOD: IODIDE ION(Non-functional Binders)

IOD.9: 7 residues within 4Å: Chain B: V.3, P.4, R.7, H.78, P.79, H.80, F.81 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, L.Y. et al., LRRK2 Roc domain RP (Ras-pocket) complexed to Divarasib. To Be Published

Release Date

2024-12-11

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