MolNFT v1 · #72547 · protein
X-ray structure of ketohexokinase in complex with a pyrazole compound
3NBW: “X-ray structure of ketohexokinase in complex with a pyrazole compound”. X-ray diffraction, 2 ligands (TR4, SO4), 5 pockets (best druggability 0.79). MolNFT v1 #72547 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3NBW
- 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
- Ligands
- TR4, SO4
- Pockets
- 5 · best druggability 0.79
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 | — |
| B | Ketohexokinase (EC 2.7.1.3) | protein | 301 | 36% helix, 25% strand | — |
Ligands and binding sites
- TR4 · 5-amino-3-(methylsulfanyl)-1-phenyl-1H-pyrazole-4-carbonitrile · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.79 | 0.84 | 65 | GOL, SO4, TR4 |
| 2 | 827 | 0.75 | 0.79 | 87 | SO4, TR4 |
| 3 | 132 | 0.43 | 0.76 | 22 | empty |
| 4 | 97 | 0.41 | 0.77 | 17 | empty |
| 5 | 53 | 0.28 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1678 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3NBW · X-ray structure of ketohexokinase in complex with a pyrazole compound · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3NBW · PDBe 3NBW
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