SMTL ID : 9m3u.1

Crystal structure of human pyruvate dehydrogenase kinase isoform 2 in complex with ATP competitive inhibitor 24

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

Ligands

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 7 residues within 4Å: Chain A: D.267, Q.325, G.326, Y.343, L.344, K.345 Chain B: L.281 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.266, A:K.345 Water bridges: A:K.345, B:R.282 EDO.2: 5 residues within 4Å: Chain A: R.150, S.227, H.228, H.231, Y.320 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.150, A:S.227, A:Y.320 EDO.3: 2 residues within 4Å: Chain A: V.101, R.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.104, A:R.104, A:N.105 EDO.7: 4 residues within 4Å: Chain A: R.242, A.243, E.246 Ligands: 01.6 No protein-ligand interaction detected (PLIP) EDO.8: 7 residues within 4Å: Chain A: L.281 Chain B: D.267, Q.325, G.326, Y.343, L.344, K.345 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.266, B:K.345 Water bridges: B:K.345, A:R.282 EDO.9: 5 residues within 4Å: Chain B: R.150, S.227, H.228, H.231, Y.320 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.150, B:S.227, B:Y.320 EDO.10: 2 residues within 4Å: Chain B: V.101, R.104 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.104, B:R.104, B:N.105 EDO.14: 4 residues within 4Å: Chain B: R.242, A.243, E.246 Ligands: 01.13 No protein-ligand interaction detected (PLIP)

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

TF3.4: 11 residues within 4Å: Chain A: P.56, R.58, V.59, V.65, M.114, G.117, V.118, Y.121, N.134, I.135, L.139 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:P.56, A:V.59, A:V.59, A:V.65, A:V.118, A:Y.121, A:I.135, A:L.139 Hydrogen bonds: A:R.58, A:R.58 Water bridges: A:N.134 pi-Cation interactions: A:R.58 TF3.11: 11 residues within 4Å: Chain B: P.56, R.58, V.59, V.65, M.114, G.117, V.118, Y.121, N.134, I.135, L.139 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:P.56, B:V.59, B:V.59, B:V.65, B:V.118, B:Y.121, B:I.135, B:L.139 Hydrogen bonds: B:R.58, B:R.58 Water bridges: B:N.134 pi-Cation interactions: B:R.58

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: R.282, K.283, R.286 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.282, A:R.282, A:K.283, A:R.286, A:R.286 GOL.12: 3 residues within 4Å: Chain B: R.282, K.283, R.286 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.282, B:R.282, B:K.283, B:R.286, B:R.286

2 x 01: 2-cyano-N-[(3R)-1-[(3S)-3-ethyl-7-(ethylamino)-5-fluoranyl-2-oxidanylidene-1H-indol-3-yl]piperidin-3-yl]-2-azaspiro[3.3]heptane-6-carboxamide

01.6: 18 residues within 4Å: Chain A: L.236, N.239, A.240, R.242, A.243, M.272, S.273, D.274, V.279, L.287, Y.292, G.309, F.310, L.314, L.330, T.338, A.340 Ligands: EDO.7 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.236, A:A.240, A:A.243, A:M.272, A:V.279, A:V.279, A:L.287, A:L.287, A:F.310, A:L.330, A:T.338 Hydrogen bonds: A:D.274, A:D.274, A:T.338 Water bridges: A:N.239, A:G.278, A:G.309 01.13: 18 residues within 4Å: Chain B: L.236, N.239, A.240, R.242, A.243, M.272, S.273, D.274, V.279, L.287, Y.292, G.309, F.310, L.314, L.330, T.338, A.340 Ligands: EDO.14 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.236, B:A.240, B:A.243, B:M.272, B:V.279, B:V.279, B:L.287, B:L.287, B:F.310, B:L.330, B:T.338 Hydrogen bonds: B:D.274, B:D.274, B:T.338 Water bridges: B:N.239, B:G.278, B:G.309

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

2025-06-25

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