SMTL ID : 8xjj.1

Co-crystal structure of SOS-1 and a potent, selective and orally bioavailable SOS1 inhibitor RGT-018

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x 01: 5-[4-[[(1~{R})-1-[3-[bis(fluoranyl)methyl]-2-fluoranyl-phenyl]ethyl]amino]-2-methyl-6-morpholin-4-yl-7-oxidanylidene-pyrido[4,3-d]pyrimidin-8-yl]pyridine-2-carbonitrile

01.1: 12 residues within 4Å: Chain A: M.319, N.320, Y.325, F.331, K.339, L.342, E.343, H.346, E.347, E.350 Ligands: EDO.2, EDO.7 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:M.319, A:Y.325, A:Y.325, A:F.331, A:F.331, A:L.342, A:L.342, A:E.343, A:H.346 Hydrogen bonds: A:N.320, A:N.320 pi-Stacking: A:H.346, A:H.346 Halogen bonds: A:K.339, A:K.339

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: Y.325, E.343 Ligands: 01.1, EDO.7 No protein-ligand interaction detected (PLIP) EDO.3: 6 residues within 4Å: Chain A: A.291, S.294, R.295, E.298, L.476, S.478 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.295, A:R.295, A:E.298, A:L.476 EDO.4: 4 residues within 4Å: Chain A: I.223, R.227, E.305, L.422 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.227, A:E.305 EDO.5: 5 residues within 4Å: Chain A: D.328, F.331, E.332, K.339 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.328, A:K.339 EDO.6: 5 residues within 4Å: Chain A: E.282, E.284, Y.449, K.453, K.471 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.282, A:Y.449 EDO.7: 7 residues within 4Å: Chain A: Y.325, L.327, D.328, F.331 Ligands: 01.1, EDO.2, EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.325, A:D.328 EDO.8: 4 residues within 4Å: Chain A: V.290, A.291, S.294, P.335 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.294 EDO.9: 4 residues within 4Å: Chain A: Y.374, N.377, I.408, E.411 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.377 Water bridges: A:E.411, A:E.411 EDO.10: 4 residues within 4Å: Chain A: Y.353, F.370, G.372, T.376 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.353, A:Y.353, A:T.376 EDO.11: 5 residues within 4Å: Chain A: T.273, L.274, E.277, S.317, S.321 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.320 EDO.12: 3 residues within 4Å: Chain A: T.46, V.47, I.48 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.46, A:V.47, A:I.48 EDO.13: 7 residues within 4Å: Chain A: P.96, T.97, D.100, S.112, A.113, E.114, L.115 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.97, A:T.97, A:S.112, A:E.114, A:L.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiao, F. et al., Discovery of RGT-018: A Potent, Selective, and Orally Bioavailable SOS1 Inhibitor for KRAS-Driven Cancers. Mol.Cancer Ther. (2024)

Release Date

2024-08-14

Peptides

Son of sevenless homolog 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Son of sevenless homolog 1