Research workbench
Structure of human ketohexokinase complexed with hits from fragment screening
Analyse Structure of human ketohexokinase complexed with hits from fragment screening in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WBZ
- Type
- protein
- Length
- 597 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ketohexokinase
- EC
- 2.7.1.3
- UniProt
- P50053
- Ligands
- A4J, SO4
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ketohexokinase (EC 2.7.1.3) | protein | 296 | 36% helix, 25% strand | P50053 |
| B | Ketohexokinase (EC 2.7.1.3) | protein | 301 | 35% helix, 25% strand | P50053 |
Ligands and binding sites
- A4J · 6-[(3S,4S)-3,4-dihydroxypyrrolidin-1-yl]-2-[(3S)-3-hydroxy-3-methylpyrrolidin-1-yl]-4-(trifluoromethyl) pyridine-3-carbonitrile · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
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 | 668 | 0.78 | 0.83 | 65 | A4J, SO4, CIT |
| 2 | 827 | 0.75 | 0.79 | 93 | A4J, SO4 |
| 3 | 132 | 0.43 | 0.76 | 21 | empty |
| 4 | 89 | 0.40 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1697 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5WBZ · Structure of human Ketohexokinase complexed with hits from fragment screening · the same entry in another collection · chain A against A, TM-score 1.00
- P50053 · AlphaFold monomer V2.0 prediction for ketohexokinase (P50053) · 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 P50053
- Elsewhere: RCSB PDB 5WBZ · PDBe 5WBZ · UniProt P50053
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