MolNFT v1 · #77746 · protein
X-ray structure of ketohexokinase in complex with an indazole compound derivative
3RO4: “X-ray structure of ketohexokinase in complex with an indazole compound derivative”. X-ray diffraction, 2 ligands (LJ9, SO4), 8 pockets (best druggability 0.76). MolNFT v1 #77746 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3RO4
- Type
- protein
- Length
- 587 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
- LJ9, SO4
- Pockets
- 8 · best druggability 0.76
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 | 291 | 36% helix, 25% strand | P50053 |
Ligands and binding sites
- LJ9 · 3-ethyl-6-[(3aR,6aS)-hexahydropyrrolo[3,4-c]pyrrol-2(1H)-yl]-1-phenyl-1H-indazole · ligand · chains A, B
- SO4 · Sulfate ion · ion · 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 | 641 | 0.76 | 0.82 | 62 | SO4, LJ9 |
| 2 | 654 | 0.65 | 0.75 | 67 | SO4 |
| 3 | 50 | 0.62 | 0.94 | 21 | empty |
| 4 | 170 | 0.48 | 0.76 | 22 | empty |
| 5 | 68 | 0.47 | 0.84 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1670 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3RO4 · X-ray Structure of Ketohexokinase in complex with an indazole compound derivative · 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 3RO4 · PDBe 3RO4 · UniProt P50053
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