MolNFT v1 · #138208 · protein
Structure of human ketohexokinase complexed with hits from fragment screening
5WBR: “Structure of human ketohexokinase complexed with hits from fragment screening”. X-ray diffraction, 2 ligands (A3Y, SO4), 4 pockets (best druggability 0.79). MolNFT v1 #138208 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5WBR
- 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
- A3Y, SO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ketohexokinase (EC 2.7.1.3) | protein | 296 | 36% helix, 24% strand | P50053 |
| B | Ketohexokinase (EC 2.7.1.3) | protein | 301 | 35% helix, 24% strand | P50053 |
Ligands and binding sites
- A3Y · 6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-[(3S)-3-(hydroxymethyl)piperidin-1-yl]-4-(trifluoromethyl) pyridine-3-carbonitrile · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- CIT · Citric acid · additive · chains A, B
- GOL · Glycerol · additive · 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 | 691 | 0.79 | 0.84 | 66 | A3Y, SO4, CIT |
| 2 | 1002 | 0.75 | 0.78 | 93 | A3Y, SO4 |
| 3 | 84 | 0.42 | 0.79 | 16 | GOL |
| 4 | 50 | 0.30 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1709 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 5WBR · 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 5WBR · PDBe 5WBR · UniProt P50053
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