MolNFT v1 · #161596 · protein
Structure of human galactokinase 1 bound with 4-{[2-(methylsulfonyl)- 1H-imidazol-1-YL]METHYL}-1,3-thiazole
6QJE: “Structure of human galactokinase 1 bound with 4-{[2-(methylsulfonyl)- 1H-imidazol-1-YL]METHYL}-1,3-thiazole”. X-ray diffraction, 4 ligands (HFK, J4Q, GAL), 17 pockets (best druggability 0.83). MolNFT v1 #161596 on GenesisL1: 3D…
- PDB
- 6QJE
- Type
- protein
- Length
- 1,518 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactokinase
- EC
- 2.7.1.6
- UniProt
- P51570
- Ligands
- HFK, J4Q, GAL, SO4
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactokinase (EC 2.7.1.6) | protein | 390 | 42% helix, 24% strand | P51570 |
| B | Galactokinase (EC 2.7.1.6) | protein | 392 | 40% helix, 24% strand | P51570 |
| C | Galactokinase (EC 2.7.1.6) | protein | 384 | 40% helix, 23% strand | P51570 |
| D | Galactokinase (EC 2.7.1.6) | protein | 352 | 36% helix, 25% strand | P51570 |
Ligands and binding sites
- HFK · 2-(1,3-benzoxazol-2-ylamino)spiro[1,6,7,8-tetrahydroquinazoline-4,1'-cyclohexane]-5-one · ligand · 3 copies · chains A, B, C
- J4Q · 4-[(2-methylsulfonylimidazol-1-yl)methyl]-1,3-thiazole · ligand · 3 copies · chains A, B, D
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.83 | 0.84 | 71 | SO4 |
| 2 | 387 | 0.77 | 0.87 | 57 | GAL, HFK |
| 3 | 338 | 0.75 | 0.87 | 54 | GAL, HFK |
| 4 | 545 | 0.72 | 0.81 | 56 | GAL, HFK |
| 5 | 202 | 0.68 | 0.86 | 37 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1051 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 562 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 291 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6QJE · Structure of human galactokinase 1 bound with 4-{[2-(Methylsulfonyl)-1H-imidazol-1-yl]meth… · the same entry in another collection · chain D against D, TM-score 1.00
- P51570 · AlphaFold monomer V2.0 prediction for galactokinase (P51570) · a predicted model of the same protein · 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
- Every structure of UniProt P51570
- Elsewhere: RCSB PDB 6QJE · PDBe 6QJE · UniProt P51570
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