SMTL ID : 9di9.1

Rat branched chain ketoacid dehydrogenase kinase in complex with inhibitor

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: 21 residues within 4Å: Chain A: N.249, A.250, A.253, D.285, G.289, I.290, V.298, F.303, T.304, T.305, G.335, F.336, G.337, F.338, G.339, L.340, P.341, T.364 Ligands: MG.2, K.3, PO4.5 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:G.335, A:F.336, A:G.337, A:G.337, A:G.339, A:L.340, A:T.364 Water bridges: A:A.250, A:R.252, A:A.253, A:D.285 Salt bridges: A:R.252 ADP.6: 21 residues within 4Å: Chain B: N.249, A.250, A.253, D.285, G.289, I.290, V.298, F.303, T.304, T.305, G.335, F.336, G.337, F.338, G.339, L.340, P.341, T.364 Ligands: MG.7, K.8, PO4.10 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:G.335, B:F.336, B:G.337, B:G.337, B:G.339, B:L.340 Water bridges: B:A.250, B:R.252, B:A.253, B:D.285, B:T.364 Salt bridges: B:R.252

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: N.249 Ligands: ADP.1, PO4.5 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: N.249 Ligands: ADP.6, PO4.10 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 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:V.298, A:D.300, A:F.303 K.8: 6 residues within 4Å: Chain B: V.298, D.300, F.303, G.337, P.341 Ligands: ADP.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:V.298, B:D.300, B:F.303

2 x 01: (3M)-6-fluoro-3-(2,4,5-trifluoro-3-methoxyphenyl)-1-benzothiophene-2-carboxylic acid

01.4: 15 residues within 4Å: Chain A: L.68, I.72, R.75, Y.99, A.102, L.106, V.125, L.128, L.129, H.132, T.163, R.167, I.170, R.171, A.174 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.68, A:I.72, A:L.106, A:L.128, A:L.128, A:I.170 Hydrogen bonds: A:Y.99 Salt bridges: A:H.132, A:R.167, A:R.171 pi-Stacking: A:Y.99 pi-Cation interactions: A:H.132 Halogen bonds: A:I.72, A:Y.99 01.9: 15 residues within 4Å: Chain B: L.68, I.72, R.75, Y.99, A.102, L.106, V.125, L.128, L.129, H.132, T.163, R.167, I.170, R.171, A.174 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.68, B:I.72, B:L.106, B:L.128, B:L.128, B:I.170 Salt bridges: B:H.132, B:R.167, B:R.171 pi-Stacking: B:Y.99 pi-Cation interactions: B:H.132 Halogen bonds: B:I.72, B:Y.99

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 7 residues within 4Å: Chain A: E.245, F.336, G.337, F.338, G.339 Ligands: ADP.1, MG.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.241, A:E.245, A:E.245, A:E.245, A:F.336, A:G.337, A:F.338, A:G.339 Water bridges: A:R.252 Salt bridges: A:K.248 PO4.10: 7 residues within 4Å: Chain B: E.245, F.336, G.337, F.338, G.339 Ligands: ADP.6, MG.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.245, B:E.245, B:F.336, B:G.337, B:F.338, B:G.339 Water bridges: B:N.249, B:R.252 Salt bridges: B:K.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Filipski, K.J. et al., Discovery of First Branched-Chain Ketoacid Dehydrogenase Kinase (BDK) Inhibitor Clinical Candidate PF-07328948. J.Med.Chem. (2024)

Release Date

2024-11-27

Peptides

Branched-chain alpha-ketoacid dehydrogenase kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Branched-chain alpha-ketoacid dehydrogenase kinase

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