SMTL ID : 9m3t.1

Crystal structure of human pyruvate dehydrogenase kinase isoform 2 in complex with ATP competitive inhibitor 22

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-dimer

Ligands

2 x TF3: N-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL)OXY]PHENYL} ACETAMIDE(Non-covalent)

TF3.1: 13 residues within 4Å: Chain A: L.56, P.57, R.59, V.60, V.66, M.115, G.118, V.119, Y.122, N.135, I.136, L.140, Y.367 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.56, A:V.60, A:V.60, A:V.66, A:V.119, A:Y.122, A:I.136, A:L.140 Hydrogen bonds: A:R.59 TF3.5: 13 residues within 4Å: Chain B: L.56, P.57, R.59, V.60, V.66, M.115, G.118, V.119, Y.122, N.135, I.136, L.140, Y.367 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.56, B:V.60, B:V.60, B:V.66, B:V.119, B:Y.122, B:I.136, B:L.140 Hydrogen bonds: B:R.59

2 x 01: 2-chloranyl-4-[[(3R)-1-[(3S)-7-(ethylamino)-5-fluoranyl-3-methyl-2-oxidanylidene-1H-indol-3-yl]piperidin-3-yl]amino]benzoic acid

01.2: 15 residues within 4Å: Chain A: L.237, N.240, A.241, A.244, M.273, D.275, V.280, K.284, R.287, L.288, A.309, F.311, L.315, L.331, T.339 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:N.240, A:A.241, A:M.273, A:V.280, A:L.288, A:L.288, A:A.309, A:F.311, A:L.331 Hydrogen bonds: A:D.275, A:D.275, A:A.309, A:T.339 Water bridges: A:G.279, A:K.284 Salt bridges: A:K.284, A:R.287 01.6: 15 residues within 4Å: Chain B: L.237, N.240, A.241, A.244, M.273, D.275, V.280, K.284, R.287, L.288, A.309, F.311, L.315, L.331, T.339 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:N.240, B:A.241, B:M.273, B:V.280, B:L.288, B:L.288, B:A.309, B:F.311, B:L.331 Hydrogen bonds: B:D.275, B:D.275, B:A.309, B:T.339 Water bridges: B:G.279, B:K.284 Salt bridges: B:K.284, B:R.287

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

DMS.3: 5 residues within 4Å: Chain A: F.24, S.34, L.38, L.153, Q.156 No protein-ligand interaction detected (PLIP) DMS.4: 5 residues within 4Å: Chain A: F.289, Q.330, L.331 Chain B: F.332 Ligands: DMS.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.331 pi-Cation interactions: A:F.332 DMS.7: 5 residues within 4Å: Chain B: F.24, S.34, L.38, L.153, Q.156 No protein-ligand interaction detected (PLIP) DMS.8: 5 residues within 4Å: Chain A: F.332 Chain B: F.289, Q.330, L.331 Ligands: DMS.4 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B pi-Cation interactions: A:F.332 Hydrogen bonds: B:L.331

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

2025-06-11

Peptides

[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial