SMTL ID : 9m3o.1

Crystal structure of human pyruvate dehydrogenase kinase isoform 1 in complex with ATP competitive inhibitor 8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

2 x K: POTASSIUM ION(Non-covalent)

K.1: 6 residues within 4Å: Chain A: A.10, R.11, F.12, N.49, V.362, Y.363 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.10, A:F.12, A:Y.363, H2O.8 K.6: 6 residues within 4Å: Chain B: A.10, R.11, F.12, N.49, V.362, Y.363 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.10, B:F.12, B:Y.363, H2O.17

2 x 01: 6-fluoranyl-8-(methylamino)-N-(pyrimidin-5-ylmethyl)-9H-pyrido[2,3-b]indole-3-carboxamide

01.2: 15 residues within 4Å: Chain A: L.240, N.243, A.244, A.247, M.276, D.278, G.282, V.283, P.284, K.287, L.291, L.319, L.335, T.343, A.345 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.240, A:N.243, A:V.283, A:V.283, A:L.291, A:L.319 Hydrogen bonds: A:D.278, A:D.278, A:K.287, A:T.343 01.7: 15 residues within 4Å: Chain B: L.240, N.243, A.244, A.247, M.276, D.278, G.282, V.283, P.284, K.287, L.291, L.319, L.335, T.343, A.345 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.240, B:N.243, B:V.283, B:V.283, B:L.291, B:L.319 Hydrogen bonds: B:D.278, B:D.278, B:D.278, B:K.287 Water bridges: B:T.343, B:T.343

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: R.286, K.287, R.290 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.286, A:R.286, A:K.287, A:R.290, A:R.290 GOL.4: 6 residues within 4Å: Chain A: D.142, M.146, L.324, Q.327, R.359 Chain B: W.380 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.142, A:D.142, A:R.359, A:R.359 Water bridges: A:R.323, A:Q.327 GOL.5: 6 residues within 4Å: Chain A: N.180, C.183, N.184, E.187, V.188, P.230 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.180, A:N.184 GOL.8: 3 residues within 4Å: Chain B: R.286, K.287, R.290 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.286, B:R.286, B:K.287, B:R.290, B:R.290 GOL.9: 6 residues within 4Å: Chain A: W.380 Chain B: D.142, M.146, L.324, Q.327, R.359 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.142, B:R.359, B:R.359 Water bridges: B:R.323, B:Q.327 GOL.10: 6 residues within 4Å: Chain B: N.180, C.183, N.184, E.187, V.188, P.230 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.180, B:N.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, H. et al., Discovery of ATP competitive PDHK1/2 dual inhibitors. Bioorg.Med.Chem.Lett. (2025)

Release Date

2025-04-02

Peptides

[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 1, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 1, mitochondrial

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