MolNFT v1 · #126492 · protein
Application of off-rate screening in the identification of novel pan- isoform inhibitors of pyruvate dehydrogenase kinase
5M4M · [pyruvate dehydrogenase (acetyl-transferring)] kinase…: “Application of off-rate screening in the identification of novel pan- isoform inhibitors of pyruvate…”. X-ray diffraction, 3 ligands (7FW, TF3, CL), 3 pockets (best…
- PDB
- 5M4M
- Type
- protein
- Length
- 344 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
- 7FW, TF3, CL
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 54% 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 | 344 | 54% helix, 15% strand | Q15119 |
Ligands and binding sites
- 7FW · ~{N}-[4-[methyl(quinoxalin-6-ylmethyl) carbamoyl]phenyl]-2,4-bis(oxidanyl)-~{N}-(phenylmethyl)benzamide · ligand · chains A
- TF3 · N-(2-aminoethyl)-2-{3-chloro-4-[(4-isopropylbenzyl) oxy]phenyl} acetamide · ligand · chains A
- CL · Chloride ion · ion · 3 copies · 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 | 137 | 0.65 | 0.87 | 23 | TF3 |
| 2 | 250 | 0.62 | 0.81 | 30 | 7FW |
| 3 | 130 | 0.40 | 0.74 | 22 | empty |
Compared structures
- 5M4M · Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors… · 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 5M4M · PDBe 5M4M · UniProt Q15119
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