SMTL ID : 9m3p.1

Crystal structure of human pyruvate dehydrogenase kinase isoform 1 in complex with ATP competitive inhibitor 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 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.7: 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.18

4 x SZ6: N-[4-(2-chloro-5-methylpyrimidin-4-yl)phenyl]-N-(4-{[(difluoroacetyl)amino]methyl}benzyl)-2,4-dihydroxybenzamide(Non-covalent)

SZ6.2: 17 residues within 4Å: Chain A: L.240, K.242, N.243, R.246, A.247, E.250, H.251, D.278, G.280, G.282, V.283, L.291, L.312, A.313, L.335, T.343, A.345 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:A.247, A:L.291, A:L.291, A:L.335 Hydrogen bonds: A:K.242, A:N.243, A:R.246, A:E.250, A:G.282, A:T.343 Water bridges: A:A.244, A:R.246, A:E.250, A:D.278, A:D.278 pi-Cation interactions: A:R.246 SZ6.3: 12 residues within 4Å: Chain A: S.15, P.16, L.17, Q.21, F.25, T.34, S.35, F.38, L.154, Q.157, L.161 Chain B: P.383 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.17, A:F.25, A:F.25, A:F.25, A:T.34, A:F.38, A:F.38 Hydrogen bonds: A:P.16 pi-Stacking: A:F.25, A:F.38 Halogen bonds: A:L.154 SZ6.8: 17 residues within 4Å: Chain B: L.240, K.242, N.243, R.246, A.247, E.250, H.251, D.278, G.280, G.282, V.283, L.291, L.312, A.313, L.335, T.343, A.345 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.247, B:L.291, B:L.291, B:L.335 Hydrogen bonds: B:K.242, B:N.243, B:R.246, B:H.251, B:G.282 Water bridges: B:A.244, B:R.246, B:E.250, B:D.278, B:T.343 pi-Cation interactions: B:R.246 SZ6.9: 12 residues within 4Å: Chain A: P.383 Chain B: S.15, P.16, L.17, Q.21, F.25, T.34, S.35, F.38, L.154, Q.157, L.161 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.17, B:F.25, B:F.25, B:F.25, B:T.34, B:F.38, B:F.38 Hydrogen bonds: B:P.16 pi-Stacking: B:F.25, B:F.38 Halogen bonds: B:L.154

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: N.180, N.182, C.183, N.184, E.187, V.188, P.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.180, A:N.182, A:N.184 GOL.5: 9 residues within 4Å: Chain A: Q.262, S.277, D.278, L.338, Y.341, G.342, T.343, D.344 Chain B: K.275 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.262, A:D.278, A:D.278, B:K.275, B:K.275 GOL.6: 6 residues within 4Å: Chain A: D.142, M.146, L.324, Q.327, R.359 Chain B: W.380 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.142, A:R.359 Water bridges: A:Q.327, A:Q.327 GOL.10: 7 residues within 4Å: Chain B: N.180, N.182, C.183, N.184, E.187, V.188, P.230 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.182, B:N.184 GOL.11: 9 residues within 4Å: Chain A: K.275 Chain B: Q.262, S.277, D.278, L.338, Y.341, G.342, T.343, D.344 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.275, A:K.275, B:Q.262, B:D.278, B:D.278, B:Y.341 GOL.12: 6 residues within 4Å: Chain A: W.380 Chain B: D.142, M.146, L.324, Q.327, R.359 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.142, B:R.359 Water bridges: B:Q.327, B:Q.327

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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