MolNFT v1 · #177222 · protein
Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with compound 7
7EBG · [pyruvate dehydrogenase (acetyl-transferring)] kinase…: “Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with compound 7”. X-ray diffraction, 4 ligands (J0L, ADP, MG), 5 pockets (best druggability 0.73). MolNFT…
- PDB
- 7EBG
- Type
- protein
- Length
- 686 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
- J0L, ADP, MG, SO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 56% 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 | 337 | 57% helix, 15% strand | Q16654 |
| B | [pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial (EC 2.7.11.2) | protein | 349 | 54% helix, 15% strand | Q16654 |
Ligands and binding sites
- J0L · 3,3-dimethyl-7-(methylamino)-1H-indol-2-one · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · chains B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 563 | 0.73 | 0.81 | 70 | SO4, MG, ADP |
| 2 | 239 | 0.62 | 0.82 | 29 | empty |
| 3 | 119 | 0.53 | 0.82 | 22 | J0L |
| 4 | 183 | 0.44 | 0.74 | 30 | empty |
| 5 | 94 | 0.37 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1499 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7EBG · Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with compound 7 · 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 7EBG · PDBe 7EBG · UniProt Q16654
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