SMTL ID : 7vbx.1

Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 20

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 5 residues within 4Å: Chain A: Y.75, H.110, V.113, R.149 Ligands: ACT.2 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain B: Y.75, H.110, V.113, R.149 Ligands: ACT.7 Ligand excluded by PLIP

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 8 residues within 4Å: Chain A: I.106, R.107, H.110, R.149, I.152, R.153, I.156 Ligands: CL.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.106, A:H.110, A:I.152 Salt bridges: A:H.110, A:R.149, A:R.153 ACT.7: 8 residues within 4Å: Chain B: I.106, R.107, H.110, R.149, I.152, R.153, I.156 Ligands: CL.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.106, B:H.110, B:I.152 Salt bridges: B:H.110, B:R.149, B:R.153

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 7 residues within 4Å: Chain A: F.23, F.26, S.36, F.39, L.40, L.155, Q.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.36 DMS.4: 6 residues within 4Å: Chain A: V.62, V.68, M.117, G.120, V.121, L.142 No protein-ligand interaction detected (PLIP) DMS.8: 7 residues within 4Å: Chain B: F.23, F.26, S.36, F.39, L.40, L.155, Q.158 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.36 DMS.9: 6 residues within 4Å: Chain B: V.62, V.68, M.117, G.120, V.121, L.142 No protein-ligand interaction detected (PLIP)

2 x 5ZP: (3~{S})-3-[5-(8-cyclopropyl-2-methyl-9~{H}-pyrido[2,3-b]indol-3-yl)-1,3,4-oxadiazol-2-yl]-4-methyl-~{N}-[(1~{R})-1-phenylethyl]pentanamide(Non-covalent)

5ZP.5: 19 residues within 4Å: Chain A: L.239, N.242, A.243, R.245, A.246, E.249, M.275, D.277, G.279, G.281, V.282, K.286, R.289, L.290, L.317, L.333, T.341, D.342, A.343 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.239, A:N.242, A:A.243, A:R.245, A:V.282, A:V.282, A:K.286, A:R.289, A:L.290, A:L.290, A:L.317, A:L.333, A:T.341, A:A.343 Hydrogen bonds: A:D.277 Water bridges: A:N.242, A:T.341, A:T.341 5ZP.10: 19 residues within 4Å: Chain B: L.239, N.242, A.243, R.245, A.246, E.249, M.275, D.277, G.279, G.281, V.282, K.286, R.289, L.290, L.317, L.333, T.341, D.342, A.343 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.239, B:N.242, B:A.243, B:R.245, B:V.282, B:V.282, B:K.286, B:R.289, B:L.290, B:L.290, B:L.317, B:L.333, B:T.341, B:A.343 Hydrogen bonds: B:D.277 Water bridges: B:N.242, B:T.341, B:T.341

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bessho, Y. et al., Structure-based drug design of novel and highly potent pyruvate dehydrogenase kinase inhibitors. Bioorg.Med.Chem. (2021)

Release Date

2022-02-16

Peptides

[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial

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