SMTL ID : 7rsj.1

Structure of the VPS34 kinase domain with compound 14

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

monomer

Ligands

3 x NA: SODIUM ION(Non-functional Binders)

NA.1: 5 residues within 4Å: Chain A: I.338, T.341, A.342, L.354, F.355 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.341, A:T.341, A:F.355 NA.2: 2 residues within 4Å: Chain A: R.118, R.215 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.118, A:R.215 NA.3: 1 residues within 4Å: Chain A: Y.545 No protein-ligand interaction detected (PLIP)

1 x 7IH: N-{4-[(7R,8R)-4-oxo-7-(propan-2-yl)-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrazin-2-yl]pyridin-2-yl}cyclopropanecarboxamide(Non-covalent)

7IH.4: 14 residues within 4Å: Chain A: I.367, K.369, Y.403, M.415, Q.416, F.417, I.418, S.420, P.422, L.483, I.493, D.494 Ligands: GOL.6, GOL.7 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.367, A:F.417, A:L.483, A:I.493, A:I.493 Hydrogen bonds: A:K.369, A:I.418, A:I.418, A:D.494 Water bridges: A:D.494, A:F.495 pi-Stacking: A:Y.403

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

EDO.5: 8 residues within 4Å: Chain A: L.400, T.401, P.402, Y.403, K.404, Q.416, I.418, K.489 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.404, A:Q.416 Water bridges: A:K.404

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: L.349, K.369, D.372, D.494 Ligands: 7IH.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.369, A:K.369, A:D.494 Water bridges: A:D.377 GOL.7: 6 residues within 4Å: Chain A: F.345, P.422, D.480, L.483, I.493 Ligands: 7IH.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, D.X. et al., Structure-Based Design of Potent, Selective, and Orally Bioavailable VPS34 Kinase Inhibitors. J.Med.Chem. (2022)

Release Date

2021-11-24

Peptides

Phosphatidylinositol 3-kinase catalytic subunit type 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphatidylinositol 3-kinase catalytic subunit type 3

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