MolNFT v1 · #177223 · protein
Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 13
7EBH · [pyruvate dehydrogenase (acetyl-transferring)] kinase…: “Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 13”. X-ray diffraction, 2 ligands (J0F, CL), 4 pockets (best druggability 0.63). MolNFT v1…
- PDB
- 7EBH
- Type
- protein
- Length
- 341 residues
- Chains
- 1
- 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
- J0F, CL
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 58% 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 | 341 | 58% helix, 15% strand | Q15119 |
Ligands and binding sites
- J0F · 5-bromanyl-2-methyl-6-propyl-7H-pyrrolo[2,3-d]pyrimidine · ligand · chains A
- CL · Chloride ion · ion · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.63 | 0.86 | 21 | DMS |
| 2 | 221 | 0.59 | 0.80 | 36 | J0F |
| 3 | 140 | 0.44 | 0.76 | 22 | ACT |
| 4 | 51 | 0.28 | 0.75 | 11 | empty |
Compared structures
- 7EBH · Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 13 · the same entry in another collection · chain A against A, 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 0.97
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 7EBH · PDBe 7EBH · UniProt Q15119
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