MolNFT v1 · #161268 · protein
Structure of human galactokinase 1 bound with N-(cyclobutylmethyl)-1, 5-dimethyl-1H-pyrazole-4-carboxamide
6Q8Z: “Structure of human galactokinase 1 bound with N-(cyclobutylmethyl)-1, 5-dimethyl-1H-pyrazole-4-carboxamide”. X-ray diffraction, 3 ligands (HFK, HR5, GAL), 18 pockets (best druggability 0.83). MolNFT v1 #161268 on GenesisL1: 3D…
- PDB
- 6Q8Z
- Type
- protein
- Length
- 1,541 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, HR5, GAL
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactokinase (EC 2.7.1.6) | protein | 392 | 42% helix, 23% strand | P51570 |
| B | Galactokinase (EC 2.7.1.6) | protein | 387 | 40% helix, 23% strand | P51570 |
| C | Galactokinase (EC 2.7.1.6) | protein | 386 | 42% helix, 23% strand | P51570 |
| D | Galactokinase (EC 2.7.1.6) | protein | 376 | 44% helix, 24% 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
- HR5 · ~{N}-(cyclobutylmethyl)-1,5-dimethyl-pyrazole-4-carboxamide · ligand · 3 copies · chains A, B, C
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.83 | 0.85 | 73 | HR5 |
| 2 | 411 | 0.77 | 0.86 | 60 | GAL, HFK |
| 3 | 443 | 0.76 | 0.85 | 63 | GAL, HFK |
| 4 | 418 | 0.74 | 0.84 | 55 | GAL, HFK |
| 5 | 204 | 0.73 | 0.89 | 33 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1047 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 561 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 276 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6Q8Z · Structure of human galactokinase 1 bound with N-(Cyclobutylmethyl)-1,5-dimethyl-1H-pyrazol… · 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 6Q8Z · PDBe 6Q8Z · UniProt P51570
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.