MolNFT v1 · #177217 · protein
Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with compound 2
7EBB · [pyruvate dehydrogenase (acetyl-transferring)] kinase…: “Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with compound 2”. X-ray diffraction, 4 ligands (42A, ADP, MG), 11 pockets (best druggability 0.73).…
- PDB
- 7EBB
- Type
- protein
- Length
- 697 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- [pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial
- EC
- 2.7.11.2
- UniProt
- Q16654
- Ligands
- 42A, ADP, MG, SO4
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | [pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial (EC 2.7.11.2) | protein | 338 | 58% helix, 15% strand | Q16654 |
| B | [pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial (EC 2.7.11.2) | protein | 359 | 53% helix, 14% strand | Q16654 |
Ligands and binding sites
- 42A · 1H-pyrrolo[2,3-b]pyridine-3-carbonitrile · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · chains B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.73 | 0.81 | 66 | SO4, MG, ADP |
| 2 | 265 | 0.58 | 0.78 | 30 | empty |
| 3 | 62 | 0.56 | 0.88 | 16 | empty |
| 4 | 144 | 0.54 | 0.81 | 26 | 42A |
| 5 | 73 | 0.52 | 0.84 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1510 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 7EBB · Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with compound 2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q16654 · AlphaFold monomer V2.0 prediction for [pyruvate dehydrogenase (acetyl-transferring)]… · a predicted model of the same protein · chain A 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 Q16654
- Elsewhere: RCSB PDB 7EBB · PDBe 7EBB · UniProt Q16654
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