SMTL ID : 9m3r.1

Crystal structure of human pyruvate dehydrogenase kinase isoform 1 in complex with ATP competitive inhibitor 29

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-dimer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: R.282, K.283, R.286 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.282, A:K.283, A:R.286 SO4.5: 6 residues within 4Å: Chain A: R.150, N.154, H.228, H.231, Y.312, Y.320 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.154, A:Y.320, A:Y.320 Salt bridges: A:R.150, A:H.228 SO4.7: 3 residues within 4Å: Chain B: R.282, K.283, R.286 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.282, B:K.283, B:R.286 SO4.11: 6 residues within 4Å: Chain B: R.150, N.154, H.228, H.231, Y.312, Y.320 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.154, B:Y.320, B:Y.320 Salt bridges: B:R.150, B:H.228

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

TF3.2: 12 residues within 4Å: Chain A: L.55, P.56, R.58, V.59, M.114, G.117, V.118, Y.121, N.134, I.135, L.139, Y.366 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.56, A:V.59, A:V.59, A:V.118, A:Y.121, A:N.134, A:I.135, A:L.139 Hydrogen bonds: A:R.58, A:R.58, A:Y.366 TF3.8: 12 residues within 4Å: Chain B: L.55, P.56, R.58, V.59, M.114, G.117, V.118, Y.121, N.134, I.135, L.139, Y.366 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:P.56, B:V.59, B:V.59, B:V.118, B:Y.121, B:N.134, B:I.135, B:L.139 Hydrogen bonds: B:R.58, B:R.58, B:Y.366

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

EDO.3: 7 residues within 4Å: Chain A: E.266, D.267, Q.325, G.326, L.344, K.345 Chain B: L.281 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.266, A:K.345 Water bridges: A:Q.325, A:K.345, B:R.282 EDO.9: 7 residues within 4Å: Chain A: L.281 Chain B: E.266, D.267, Q.325, G.326, L.344, K.345 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:R.282, B:Q.325, B:K.345 Hydrogen bonds: B:E.266, B:K.345

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: V.101, R.104 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.104, A:R.104, A:T.157, A:T.157 GOL.10: 2 residues within 4Å: Chain B: V.101, R.104 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.104, B:R.104, B:T.157, B:T.157

2 x 01: 3-[4-[4-(ethylamino)-6-fluoranyl-2-oxidanylidene-3H-benzimidazol-1-yl]phenoxy]benzenesulfonyl fluoride

01.6: 15 residues within 4Å: Chain A: L.236, N.239, A.240, A.243, M.272, S.273, D.274, V.279, K.283, R.286, L.287, Y.292, L.314, L.330, T.338 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.240, A:M.272, A:V.279, A:V.279, A:K.283, A:L.287, A:L.287, A:Y.292 Hydrogen bonds: A:D.274, A:D.274, A:T.338 Water bridges: A:G.278, A:K.283 01.12: 15 residues within 4Å: Chain B: L.236, N.239, A.240, A.243, M.272, S.273, D.274, V.279, K.283, R.286, L.287, Y.292, L.314, L.330, T.338 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:A.240, B:M.272, B:V.279, B:V.279, B:K.283, B:L.287, B:L.287, B:Y.292 Hydrogen bonds: B:D.274, B:D.274, B:T.338 Water bridges: B:G.278, B:K.283

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