SMTL ID : 4v26.1

VER-246608, a novel pan-isoform ATP competitive inhibitor of pyruvate dehydrogenase kinase, disrupts Warburg metabolism and induces context- dependent cytostasis in cancer cells

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-dimer

Ligands

2 x TF3: N-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL)OXY]PHENYL} ACETAMIDE(Non-covalent)

TF3.1: 12 residues within 4Å: Chain A: L.71, P.72, R.74, V.75, V.81, G.133, V.134, Y.137, N.150, I.151, F.154, L.155 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.75, A:V.75, A:V.81, A:V.134, A:Y.137, A:I.151, A:F.154, A:L.155 Hydrogen bonds: A:R.74, A:R.74 pi-Cation interactions: A:R.74 TF3.5: 12 residues within 4Å: Chain B: L.71, P.72, R.74, V.75, V.81, G.133, V.134, Y.137, N.150, I.151, F.154, L.155 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.75, B:V.75, B:V.81, B:V.134, B:Y.137, B:I.151, B:F.154, B:L.155 Hydrogen bonds: B:R.74, B:R.74 pi-Cation interactions: B:R.74

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: Q.345, L.346 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain A: F.39, S.49 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: Q.345, L.346 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: F.39, S.49 No protein-ligand interaction detected (PLIP)

2 x 7TJ: N-[4-(2-CHLORO-5-METHYLPYRIMIDIN-4-YL)PHENYL]-2,4-DIHYDROXY-N-(4-{[(TRIFLUOROACETYL)AMINO]METHYL}BENZYL)BENZAMIDE(Non-covalent)

7TJ.4: 15 residues within 4Å: Chain A: L.252, K.254, N.255, R.258, A.259, E.262, S.263, D.290, G.292, G.294, V.295, L.303, A.324, L.346, T.354 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.259, A:L.303, A:L.346 Hydrogen bonds: A:K.254, A:N.255, A:R.258, A:E.262, A:G.294 Water bridges: A:D.290, A:T.354 pi-Cation interactions: A:R.258 7TJ.8: 15 residues within 4Å: Chain B: L.252, K.254, N.255, R.258, A.259, E.262, S.263, D.290, G.292, G.294, V.295, L.303, A.324, L.346, T.354 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:A.259, B:L.303, B:L.346 Hydrogen bonds: B:K.254, B:N.255, B:R.258, B:E.262, B:G.294 Water bridges: B:L.252, B:D.290, B:T.354 pi-Cation interactions: B:R.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moore, J.D. et al., VER-246608, a novel pan-isoform ATP competitive inhibitor of pyruvate dehydrogenase kinase, disrupts Warburg metabolism and induces context-dependent cytostasis in cancer cells. Oncotarget (2014)

Release Date

2014-12-03

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