SMTL ID : 7rsv.1 (1 other biounit)

Structure of the VPS34 kinase domain with compound 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

1 x 7IQ: (5aS,8aR,9S)-2-[(3R)-3-methylmorpholin-4-yl]-5,5a,6,7,8,8a-hexahydro-4H-cyclopenta[e]pyrazolo[1,5-a]pyrazin-4-one(Non-covalent)

7IQ.1: 14 residues within 4Å: Chain A: F.345, P.351, I.367, K.369, Y.403, M.415, Q.416, F.417, I.418, S.420, L.483, I.493, D.494 Ligands: GOL.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.345, A:F.345, A:P.351, A:M.415, A:I.493 Hydrogen bonds: A:K.369, A:K.369, A:I.418, A:D.494

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: K.369, D.372, D.494 Ligands: 7IQ.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.369, A:K.369, A:D.372 Water bridges: A:D.372, A:D.372, A:D.494 GOL.3: 2 residues within 4Å: Chain A: E.526, Q.529 No protein-ligand interaction detected (PLIP)

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

NA.4: 1 residues within 4Å: Chain A: D.142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.142 NA.5: 3 residues within 4Å: Chain A: Q.293, L.349, H.370 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.370 Water bridges: A:H.370 NA.6: 1 residues within 4Å: Chain A: T.343 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.343, A:T.343 NA.7: 0 residues within 4Å: (No contacts) 3 PLIP interactions: 3 interactions with chain A Water bridges: A:L.400, A:P.402, A:Q.416

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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