SMTL ID : 7ebg.1

Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with compound 7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: R.117, H.121, R.159, R.163 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.117 Water bridges: A:R.159, A:R.159, A:R.159 Salt bridges: A:H.121, A:R.159, A:R.163 SO4.3: 5 residues within 4Å: Chain B: R.117, H.121, R.159, R.163, N.167 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.159, B:N.167 Water bridges: B:R.117, B:R.159 Salt bridges: B:H.121, B:R.163 SO4.4: 11 residues within 4Å: Chain B: E.247, K.250, L.320, A.321, G.322, F.323, G.324, Y.325, G.326 Ligands: MG.5, ADP.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.322, B:F.323, B:G.324, B:Y.325, B:G.326 Water bridges: B:N.251, B:L.320 Salt bridges: B:K.250

1 x J0L: 3,3-dimethyl-7-(methylamino)-1H-indol-2-one(Non-covalent)

J0L.2: 12 residues within 4Å: Chain A: L.248, N.251, A.252, A.255, I.284, D.286, V.291, L.299, L.327, L.343, T.351, A.353 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:N.251, A:V.291, A:L.299, A:L.327, A:L.327, A:L.343 Hydrogen bonds: A:D.286, A:D.286, A:T.351

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain B: E.247, N.251 Ligands: SO4.4, ADP.6 No protein-ligand interaction detected (PLIP)

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.6: 21 residues within 4Å: Chain B: N.251, R.254, A.255, D.286, V.291, L.299, Y.304, S.305, T.306, A.321, G.322, F.323, G.324, Y.325, G.326, L.327, P.328, L.343, T.351 Ligands: SO4.4, MG.5 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:N.251, B:R.254, B:D.286, B:S.305, B:S.305, B:S.305, B:T.306, B:T.306, B:G.322, B:G.324, B:Y.325, B:G.326, B:L.327 Water bridges: B:A.252, B:D.286, B:T.351, B:T.351

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Akaki, T. et al., Fragment-based lead discovery to identify novel inhibitors that target the ATP binding site of pyruvate dehydrogenase kinases. Bioorg.Med.Chem. (2021)

Release Date

2021-08-04

Peptides

[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial

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