SMTL ID : 4v25.1

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 2.60 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.72, P.73, R.75, V.76, M.131, G.134, V.135, Y.138, N.151, I.152, F.155, L.156 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.72, A:V.76, A:V.76, A:V.135, A:N.151, A:I.152, A:L.156 Hydrogen bonds: A:R.75 pi-Stacking: A:Y.138 pi-Cation interactions: A:R.75 TF3.4: 12 residues within 4Å: Chain B: L.72, P.73, R.75, V.76, M.131, G.134, V.135, Y.138, N.151, I.152, F.155, L.156 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.72, B:V.76, B:V.76, B:V.135, B:N.151, B:I.152, B:L.156 Hydrogen bonds: B:R.75 pi-Stacking: B:Y.138 pi-Cation interactions: B:R.75

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: L.347 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain B: L.347 No protein-ligand interaction detected (PLIP)

2 x SZ6: N-[4-(2-chloro-5-methylpyrimidin-4-yl)phenyl]-N-(4-{[(difluoroacetyl)amino]methyl}benzyl)-2,4-dihydroxybenzamide(Non-covalent)

SZ6.3: 15 residues within 4Å: Chain A: L.253, K.255, N.256, R.259, A.260, E.263, S.264, D.291, G.293, G.295, V.296, L.304, L.324, L.347, T.355 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.260, A:L.304, A:L.347 Hydrogen bonds: A:K.255, A:N.256, A:R.259, A:E.263, A:G.295 Water bridges: A:G.293, A:T.355 pi-Cation interactions: A:R.259 SZ6.6: 15 residues within 4Å: Chain B: L.253, K.255, N.256, R.259, A.260, E.263, S.264, D.291, G.293, G.295, V.296, L.304, L.324, L.347, T.355 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.260, B:L.304, B:L.347 Hydrogen bonds: B:K.255, B:N.256, B:R.259, B:E.263, B:G.295 Water bridges: B:G.293, B:T.355 pi-Cation interactions: B:R.259

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

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