MolNFT v1 · #108278 · protein
Ver-246608, a novel pan-isoform ATP competitive inhibitor of pyruvate dehydrogenase kinase, disrupts warburg metabolism and induces context- dependent cytostasis in cancer cells
4V25 · [pyruvate dehydrogenase (acetyl-transferring)] kinase…: “Ver-246608, a novel pan-isoform ATP competitive inhibitor of pyruvate dehydrogenase kinase, disrupts warburg…”. X-ray diffraction, 3 ligands (TF3, SZ6, MG), 3 pockets (best…
- PDB
- 4V25
- Type
- protein
- Length
- 343 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- [pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
- EC
- 2.7.11.2
- UniProt
- Q15119
- Ligands
- TF3, SZ6, MG
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | [pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial (EC 2.7.11.2) | protein | 343 | 53% helix, 15% strand | Q15119 |
Ligands and binding sites
- TF3 · N-(2-aminoethyl)-2-{3-chloro-4-[(4-isopropylbenzyl) oxy]phenyl} acetamide · ligand · chains A
- SZ6 · N-[4-(2-chloro-5-methylpyrimidin-4-yl)phenyl]-N-(4-{[(difluoroacetyl)amino]methyl}benzyl)-2,4-dihydroxybenzamide · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.64 | 0.86 | 24 | TF3 |
| 2 | 376 | 0.62 | 0.77 | 44 | SZ6 |
| 3 | 101 | 0.44 | 0.78 | 17 | empty |
Compared structures
- 4V25 · VER-246608, a novel pan-isoform ATP competitive inhibitor of pyruvate dehydrogenase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q15119 · AlphaFold monomer V2.0 prediction for [pyruvate dehydrogenase (acetyl-transferring)]… · a predicted model of the same protein · chain A against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q15119
- Elsewhere: RCSB PDB 4V25 · PDBe 4V25 · UniProt Q15119
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.