MolNFT v1 · #155789 · protein
Crystal structure of human PDK2 complexed with GM10030
6LIN · [pyruvate dehydrogenase (acetyl-transferring)] kinase…: “Crystal structure of human PDK2 complexed with GM10030”. X-ray diffraction, 2 ligands (EH0, SO4), 20 pockets (best druggability 0.70). MolNFT v1 #155789 on GenesisL1: 3D…
- PDB
- 6LIN
- Type
- protein
- Length
- 1,448 residues
- Chains
- 4
- 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
- EH0, SO4
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | [pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial (EC 2.7.11.2) | protein | 365 | 51% helix, 14% strand | Q15119 |
| B | [pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial (EC 2.7.11.2) | protein | 362 | 51% helix, 14% strand | Q15119 |
| C | [pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial (EC 2.7.11.2) | protein | 367 | 51% helix, 14% strand | Q15119 |
| D | [pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial (EC 2.7.11.2) | protein | 354 | 53% helix, 14% strand | Q15119 |
Ligands and binding sites
- EH0 · 4-[[[4-[3,5-bis(fluoranyl)-4-(4-oxidanyl-4-oxidanylidene-butoxy)phenyl]-5-[5-chloranyl-2,4-bis(oxidanyl)phenyl]-1,2-oxazol-3-yl]carbonylamino]methyl]benzoic acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.70 | 0.84 | 35 | EH0 |
| 2 | 355 | 0.64 | 0.79 | 30 | empty |
| 3 | 359 | 0.63 | 0.79 | 40 | empty |
| 4 | 348 | 0.61 | 0.78 | 54 | PEG, EH0 |
| 5 | 63 | 0.56 | 0.88 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1384 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1283 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 714 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6LIN · Crystal structure of human PDK2 complexed with GM10030 · the same entry in another collection · chain D against D, TM-score 1.00
- Q15119 · AlphaFold monomer V2.0 prediction for [pyruvate dehydrogenase (acetyl-transferring)]… · a predicted model of the same protein · chain D against A, TM-score 0.99
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 6LIN · PDBe 6LIN · UniProt Q15119
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