MolNFT v1 · #56395 · protein
Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4
2ZDX · Pyruvate dehydrogenase kinase isozyme 4: “Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4”. X-ray diffraction, 1 ligand (P4A), 8 pockets (best druggability 0.62). MolNFT v1 #56395 on GenesisL1: 3D structure…
- PDB
- 2ZDX
- Type
- protein
- Length
- 681 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate dehydrogenase kinase isozyme 4
- EC
- 2.7.11.2
- UniProt
- Q16654
- Ligands
- P4A
- Pockets
- 8 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate dehydrogenase kinase isozyme 4 (EC 2.7.11.2) | protein | 337 | 54% helix, 17% strand | Q16654 |
| B | Pyruvate dehydrogenase kinase isozyme 4 (EC 2.7.11.2) | protein | 344 | 49% helix, 15% strand | Q16654 |
Ligands and binding sites
- P4A · 4-[4-(4-methoxyphenyl)-5-methyl-1H-pyrazol-3-yl]benzene-1,3-diol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.62 | 0.79 | 35 | empty |
| 2 | 166 | 0.55 | 0.80 | 25 | P4A |
| 3 | 76 | 0.51 | 0.84 | 13 | empty |
| 4 | 118 | 0.49 | 0.80 | 24 | P4A |
| 5 | 205 | 0.47 | 0.75 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 1488 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 2ZDX · Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4 · 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 0.98
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 Q16654
- Elsewhere: RCSB PDB 2ZDX · PDBe 2ZDX · UniProt Q16654
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