SMTL ID : 8f4q.1

rat branched chain ketoacid dehydrogenase kinase in complex with inhibtors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: K.248, N.249, R.252, A.253, D.285, G.289, I.290, V.298, F.303, T.304, T.305, F.336, G.337, G.339, L.340, P.341, T.364 18 PLIP interactions: 18 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:A.306, A:F.336, A:G.337, A:G.337, A:L.340 Water bridges: A:D.285, A:F.338, A:F.338, A:T.364, A:T.364 Salt bridges: A:K.248, A:R.252 ADP.7: 17 residues within 4Å: Chain B: K.248, N.249, R.252, A.253, D.285, G.289, I.290, V.298, F.303, T.304, T.305, F.336, G.337, G.339, L.340, P.341, T.364 18 PLIP interactions: 18 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:A.306, B:F.336, B:G.337, B:G.337, B:L.340 Water bridges: B:D.285, B:F.338, B:F.338, B:T.364, B:T.364 Salt bridges: B:K.248, B:R.252

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

SO4.2: 7 residues within 4Å: Chain A: S.37, R.39, R.71, H.74, R.75, K.162, S.166 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.37, A:S.166 Water bridges: A:R.71, A:R.71, A:R.75, A:R.75 Salt bridges: A:R.39, A:R.71, A:H.74, A:R.75, A:K.162 SO4.3: 3 residues within 4Å: Chain A: R.286 Chain B: N.225, G.226 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.286 Hydrogen bonds: B:G.226 SO4.8: 7 residues within 4Å: Chain B: S.37, R.39, R.71, H.74, R.75, K.162, S.166 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.37, B:S.166 Water bridges: B:R.71, B:R.71, B:R.75, B:R.75 Salt bridges: B:R.39, B:R.71, B:H.74, B:R.75, B:K.162 SO4.9: 3 residues within 4Å: Chain A: N.225, G.226 Chain B: R.286 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.226 Salt bridges: B:R.286

6 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.128 Salt bridges: A:H.132, A:R.167, A:R.171 XER.5: 8 residues within 4Å: Chain A: R.75, G.78, S.81, L.155, Y.158, F.159, K.162, T.163 6 PLIP interactions: 6 interactions with chain A Salt bridges: A:R.75, A:K.162 pi-Stacking: A:Y.158, A:Y.158 Halogen bonds: A:F.159, A:T.163 XER.6: 8 residues within 4Å: Chain A: F.207, A.208, L.211, C.212, K.215, Y.216, K.248, R.252 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.211, A:K.248 Salt bridges: A:K.215, A:R.252 XER.10: 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 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.128 Salt bridges: B:H.132, B:R.167, B:R.171 XER.11: 8 residues within 4Å: Chain B: R.75, G.78, S.81, L.155, Y.158, F.159, K.162, T.163 6 PLIP interactions: 6 interactions with chain B Salt bridges: B:R.75, B:K.162 pi-Stacking: B:Y.158, B:Y.158 Halogen bonds: B:F.159, B:T.163 XER.12: 8 residues within 4Å: Chain B: F.207, A.208, L.211, C.212, K.215, Y.216, K.248, R.252 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.211, B:K.248 Salt bridges: B:K.215, B:R.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roth Flach, R. et al., Discovery of branched-chain ketoacid dehydrogenase kinase (BDK) inhibitors acting as stabilizers or destabilizers. To Be Published

Release Date

2023-12-13

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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