MolNFT v1 · #155787 · protein
Crystal structure of human PDK2 complexed with an allosteric inhibitor compound 8C
6LIL · [pyruvate dehydrogenase (acetyl-transferring)] kinase…: “Crystal structure of human PDK2 complexed with an allosteric inhibitor compound 8C”. X-ray diffraction, 2 ligands (EGX, SO4), 8 pockets (best druggability 0.71). MolNFT v1…
- PDB
- 6LIL
- Type
- protein
- Length
- 690 residues
- Chains
- 2
- 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
- EGX, SO4
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 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 | 346 | 54% helix, 15% strand | Q15119 |
| B | [pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial (EC 2.7.11.2) | protein | 344 | 54% helix, 15% strand | Q15119 |
Ligands and binding sites
- EGX · 1-(1-piperidin-4-ylpyrazol-4-yl)anthracene-9,10-dione · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- FLC · Citrate anion · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.71 | 0.82 | 55 | FLC, PEG |
| 2 | 425 | 0.70 | 0.81 | 51 | FLC, PEG |
| 3 | 108 | 0.65 | 0.89 | 19 | EGX |
| 4 | 99 | 0.65 | 0.89 | 16 | EGX |
| 5 | 372 | 0.64 | 0.79 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 1229 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6LIL · Crystal structure of human PDK2 complexed with an allosteric inhibitor compound 8c · the same entry in another collection · chain B against B, 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 0.98
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 6LIL · PDBe 6LIL · UniProt Q15119
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