SMTL ID : 8v8j.1 (1 other biounit)

PI3Ka H1047R co-crystal structure with inhibitors in two cryptic pockets (compounds 4 and 5).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.35 Å

Oligo State

hetero-1-1-mer

Ligands

1 x YO4: 2-({(1R)-1-[2-(4,4-dimethylpiperidin-1-yl)-3,6-dimethyl-4-oxo-4H-1-benzopyran-8-yl]ethyl}amino)benzoic acid(Non-covalent)

YO4.1: 17 residues within 4Å: Chain A: C.905, C.909, T.912, F.913, G.918, H.935, F.958, T.961, F.964, F.981, F.984, Q.985, C.988, M.1047, N.1048, A.1050, R.1051 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.913, A:F.958, A:T.961, A:F.964, A:F.984, A:M.1047 Hydrogen bonds: A:Q.985, A:M.1047 Salt bridges: A:R.1051 pi-Stacking: A:F.958

1 x YOR: N-{(3S)-3-(2-methylphenyl)-6-[(oxetan-3-yl)amino]-1-oxo-2,3-dihydro-1H-isoindol-4-yl}-1-benzothiophene-3-carboxamide(Non-covalent)

YOR.2: 15 residues within 4Å: Chain A: Q.813, L.816, T.817, L.915, G.916, I.917, L.942, K.945, R.953, F.1006, E.1016, L.1017, D.1022, Y.1025, I.1026 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.816, A:L.942, A:L.942, A:F.1006, A:F.1006, A:F.1006, A:E.1016, A:L.1017, A:Y.1025, A:Y.1025, A:I.1026 Hydrogen bonds: A:L.915, A:G.916, A:K.945, A:D.1022 pi-Stacking: A:F.1006, A:Y.1025 pi-Cation interactions: A:K.945, A:K.945

1 x YNZ: (2S)-N~1~-[(4P)-2-tert-butyl-4'-methyl[4,5'-bi-1,3-thiazol]-2'-yl]pyrrolidine-1,2-dicarboxamide(Non-covalent)

YNZ.3: 14 residues within 4Å: Chain A: M.776, W.784, K.806, Y.840, E.853, V.854, V.855, N.857, S.858, H.859, Q.863, M.926, I.936, D.937 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.840, A:V.855 Hydrogen bonds: A:V.855, A:V.855, A:S.858, A:Q.863, A:Q.863

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ketcham, J.M. et al., Discovery of Pyridopyrimidinones that Selectively Inhibit the H1047R PI3K alpha Mutant Protein. J.Med.Chem. (2024)

Release Date

2024-03-20

Peptides

Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform: A
Phosphatidylinositol 3-kinase regulatory subunit alpha: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform

Phosphatidylinositol 3-kinase regulatory subunit alpha

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