MolNFT v1 · #171799 · protein
Structure of human galactokinase 1 bound with 2-(4-chlorophenyl)-N- (pyrimidin-2-YL)ACETAMIDE
6ZGZ: “Structure of human galactokinase 1 bound with 2-(4-chlorophenyl)-N- (pyrimidin-2-YL)ACETAMIDE”. X-ray diffraction, 3 ligands (HFK, SSY, GAL), 18 pockets (best druggability 0.84). MolNFT v1 #171799 on GenesisL1: 3D structure, binding…
- PDB
- 6ZGZ
- Type
- protein
- Length
- 1,534 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, SSY, GAL
- Pockets
- 18 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactokinase (EC 2.7.1.6) | protein | 388 | 39% helix, 24% strand | P51570 |
| B | Galactokinase (EC 2.7.1.6) | protein | 388 | 43% helix, 23% strand | P51570 |
| E | Galactokinase (EC 2.7.1.6) | protein | 390 | 43% helix, 24% strand | P51570 |
| D | Galactokinase (EC 2.7.1.6) | protein | 368 | 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, E
- SSY · ~{N}-(3-ethanoylphenyl)-2,2,2-tris(fluoranyl)ethanamide · ligand · chains D
- 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
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 | 1003 | 0.84 | 0.85 | 100 | empty |
| 2 | 952 | 0.83 | 0.85 | 85 | empty |
| 3 | 885 | 0.83 | 0.85 | 67 | empty |
| 4 | 436 | 0.77 | 0.86 | 52 | GAL, HFK |
| 5 | 354 | 0.77 | 0.87 | 49 | GAL, HFK |
Interfaces
5 interfaces between chains.
- A–B · 1070 Ų buried · 16 hydrogen bonds · protein-protein
- E–D · 989 Ų buried · 18 hydrogen bonds · protein-protein
- B–E · 325 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 302 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 253 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6ZGZ · 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 6ZGZ · PDBe 6ZGZ · UniProt P51570
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