MolNFT v1 · #161104 · protein
Structure of human galactokinase 1 bound with ethyl 1-(2-pyrazinyl)-4- piperidinecarboxylate
6Q3W: “Structure of human galactokinase 1 bound with ethyl 1-(2-pyrazinyl)-4- piperidinecarboxylate”. X-ray diffraction, 3 ligands (HFK, HGE, GAL), 16 pockets (best druggability 0.83). MolNFT v1 #161104 on GenesisL1: 3D structure, binding…
- PDB
- 6Q3W
- Type
- protein
- Length
- 1,523 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, HGE, GAL
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactokinase (EC 2.7.1.6) | protein | 391 | 43% helix, 23% strand | P51570 |
| B | Galactokinase (EC 2.7.1.6) | protein | 385 | 41% helix, 24% strand | P51570 |
| C | Galactokinase (EC 2.7.1.6) | protein | 390 | 41% helix, 24% strand | P51570 |
| D | Galactokinase (EC 2.7.1.6) | protein | 357 | 40% 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
- HGE · ethyl 1-pyrazin-2-ylpiperidine-4-carboxylate · ligand · chains 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
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.83 | 0.85 | 72 | empty |
| 2 | 453 | 0.77 | 0.86 | 54 | GAL, HFK |
| 3 | 393 | 0.76 | 0.86 | 47 | GAL, HFK |
| 4 | 427 | 0.69 | 0.81 | 57 | GAL, HFK |
| 5 | 181 | 0.68 | 0.87 | 34 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1060 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 268 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 257 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
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 6Q3W · PDBe 6Q3W · UniProt P51570
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.