SMTL ID : 9dkp.1

The structure of human vacuolar protein sorting 34 catalytic domain bound to RD-I-53

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

monomer

Ligands

1 x 01: (8R)-3-(1,3-benzothiazol-2-yl)pyrazolo[1,5-a]pyrimidine

01.1: 13 residues within 4Å: Chain A: I.357, Y.393, M.405, Q.406, F.407, I.408, S.410, P.412, E.415, L.473, I.483 Ligands: ETX.2, CL.20 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.407, A:P.412, A:L.473 Hydrogen bonds: A:I.408 pi-Stacking: A:Y.393

1 x ETX: 2-ETHOXYETHANOL(Non-covalent)

ETX.2: 9 residues within 4Å: Chain A: F.335, S.337, P.341, I.357, K.359, M.405, I.483, D.484 Ligands: 01.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.341 Hydrogen bonds: A:D.484 Water bridges: A:D.367

2 x ETZ: diethyl ether(Non-covalent)

ETZ.3: 5 residues within 4Å: Chain A: Y.217, R.262, L.265, A.266, Q.269 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.262, A:A.266 ETZ.4: 5 residues within 4Å: Chain A: L.264, L.313, P.315, K.323, E.349 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.264, A:K.323 Hydrogen bonds: A:K.323

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 7 residues within 4Å: Chain A: L.116, M.117, Y.219, Q.372, S.375, K.394 Ligands: CL.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.219 pi-Cation interactions: A:Y.215

2 x K: POTASSIUM ION(Non-functional Binders)

K.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

13 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 3 residues within 4Å: Chain A: K.394, V.395 Ligands: DMS.5 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: F.335, Q.343 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: M.340 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: W.40, E.67 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: E.129, N.130, D.197 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain A: Y.33 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: S.210, M.261 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain A: D.363 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain A: L.339 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain A: G.490, D.492 Ligand excluded by PLIP CL.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain A: D.233, K.235, T.236 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain A: S.410, V.411, E.415 Ligands: 01.1 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abiodun, W.O. et al., Facile Bacterial Production of Human Vacuolar Protein Sorting 34 Enables Structural Characterization of Novel Inhibitors. To Be Published

Release Date

2025-09-17

Peptides

Phosphatidylinositol 3-kinase catalytic subunit type 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Phosphatidylinositol 3-kinase catalytic subunit type 3

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