SMTL ID : 8f5f.1 (1 other biounit)

human branched chain ketoacid dehydrogenase kinase in complex with inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 20 residues within 4Å: Chain A: N.249, R.252, A.253, D.285, G.289, I.290, V.298, F.303, T.304, T.305, M.333, H.334, F.336, G.337, F.338, G.339, L.340, P.341, T.364 Ligands: MG.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.249, A:R.252, A:D.285, A:T.304, A:T.305, A:T.305, A:G.335, A:F.336, A:G.337, A:G.337, A:F.338, A:L.340, A:T.364 Water bridges: A:E.245, A:E.245, A:N.249, A:M.333, A:G.339 ADP.5: 20 residues within 4Å: Chain B: N.249, R.252, A.253, D.285, G.289, I.290, V.298, F.303, T.304, T.305, M.333, H.334, F.336, G.337, F.338, G.339, L.340, P.341, T.364 Ligands: MG.6 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:N.249, B:R.252, B:D.285, B:T.304, B:T.304, B:T.305, B:T.305, B:G.335, B:F.336, B:G.337, B:G.337, B:F.338, B:L.340 Water bridges: B:N.249, B:D.285, B:M.333, B:G.339, B:G.339, B:T.364, B:T.364

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: N.249 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: N.249 Ligands: ADP.5 No protein-ligand interaction detected (PLIP)

2 x XGG: (2P)-2-[(4P)-4-{6-[(1-ethylcyclopropyl)methoxy]pyridin-3-yl}-1,3-thiazol-2-yl]benzoic acid(Non-covalent)

XGG.3: 16 residues within 4Å: Chain A: L.68, I.72, A.102, L.106, V.125, L.128, L.129, H.132, K.133, V.136, L.164, R.167, I.170, R.171, Y.241, Y.346 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.72, A:A.102, A:L.128, A:R.167, A:I.170, A:R.171, A:Y.241 Hydrogen bonds: A:R.167, A:R.167 Water bridges: A:R.171 Salt bridges: A:R.167 pi-Cation interactions: A:R.167 XGG.7: 16 residues within 4Å: Chain B: L.68, I.72, A.102, L.106, V.125, L.128, L.129, H.132, K.133, V.136, L.164, R.167, I.170, R.171, Y.241, Y.346 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.72, B:A.102, B:L.128, B:R.167, B:I.170, B:R.171, B:Y.241 Hydrogen bonds: B:R.167, B:R.167 Water bridges: B:R.171, B:Y.346, B:Y.346 Salt bridges: B:R.167 pi-Cation interactions: B:R.167

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

SO4.4: 4 residues within 4Å: Chain A: S.37, R.39, R.71, H.74 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.37 Salt bridges: A:R.39, A:R.71, A:H.74 SO4.8: 4 residues within 4Å: Chain B: S.37, R.39, R.71, H.74 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.37 Salt bridges: B:R.39, B:R.71, B:H.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roth Flach, R.J. et al., Small molecule branched-chain ketoacid dehydrogenase kinase (BDK) inhibitors with opposing effects on BDK protein levels. Nat Commun (2023)

Release Date

2023-07-05

Peptides

[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial

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