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Structure of human galactokinase 1 bound with 2-(4-chlorophenyl)-N- (pyrimidin-2-YL)ACETAMIDE
Analyse Structure of human galactokinase 1 bound with 2-(4-chlorophenyl)-N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZGY
- Type
- protein
- Length
- 1,542 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, QL5, GAL
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Galactokinase (EC 2.7.1.6) | protein | 391 | 42% helix, 24% strand | P51570 |
| D | Galactokinase (EC 2.7.1.6) | protein | 369 | 43% 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, E
- QL5 · (2,5-dimethylphenyl) pyridine-4-carboxylate · ligand · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 963 | 0.84 | 0.85 | 84 | empty |
| 2 | 924 | 0.84 | 0.85 | 71 | empty |
| 3 | 1148 | 0.82 | 0.83 | 103 | empty |
| 4 | 423 | 0.78 | 0.87 | 56 | GAL, HFK |
| 5 | 401 | 0.77 | 0.86 | 48 | GAL, HFK |
Interfaces
5 interfaces between chains.
- A–B · 1052 Ų buried · 18 hydrogen bonds · protein-protein
- E–D · 884 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 318 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 317 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 277 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6ZGY · Structure of human galactokinase 1 bound with 2-(4-chlorophenyl)-N-(pyrimidin-2-yl)acetami… · 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 E 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 6ZGY · PDBe 6ZGY · UniProt P51570
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