SMTL ID : 8f5j.1

human branched chain ketoacid dehydrogenase kinase in complex with inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 19 residues within 4Å: Chain A: N.249, A.253, D.285, G.289, I.290, V.298, F.303, T.304, T.305, H.334, G.335, F.336, G.337, G.339, L.340, P.341, T.364 Ligands: MG.2, K.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.249, A:D.285, A:T.304, A:T.304, A:T.305, A:T.305, A:G.337, A:G.337, A:L.340 Water bridges: A:A.250, A:D.285, A:F.336, A:F.338, A:T.364, A:T.364 Salt bridges: A:H.334 ADP.5: 19 residues within 4Å: Chain B: N.249, A.253, D.285, G.289, I.290, V.298, F.303, T.304, T.305, H.334, G.335, F.336, G.337, G.339, L.340, P.341, T.364 Ligands: MG.6, K.7 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:N.249, B:D.285, B:T.304, B:T.304, B:T.305, B:T.305, B:G.337, B:G.337, B:L.340 Water bridges: B:A.250, B:D.285, B:F.336, B:F.338, B:T.364, B:T.364 Salt bridges: B:H.334

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: E.245, N.249, H.334, G.339 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain B: E.245, N.249, H.334, G.339 Ligands: ADP.5 No protein-ligand interaction detected (PLIP)

2 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: V.298, D.300, F.303, G.337, P.341 Ligands: ADP.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:V.298, A:D.300, A:F.303, A:G.337 K.7: 6 residues within 4Å: Chain B: V.298, D.300, F.303, G.337, P.341 Ligands: ADP.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:V.298, B:D.300, B:F.303, B:G.337

2 x XER: 3-chloro-5-fluorothieno[3,2-b]thiophene-2-carboxylic acid(Non-covalent)

XER.4: 12 residues within 4Å: Chain A: L.68, I.72, Y.99, L.106, V.125, L.128, L.129, H.132, R.167, I.170, R.171, A.174 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.128, A:A.174 Salt bridges: A:H.132, A:R.167, A:R.171 XER.8: 12 residues within 4Å: Chain B: L.68, I.72, Y.99, L.106, V.125, L.128, L.129, H.132, R.167, I.170, R.171, A.174 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.128, B:A.174 Salt bridges: B:H.132, B:R.167, B:R.171

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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