MolNFT v1 · #171795 · protein
Structure of human galactokinase 1 bound with 2-(4-chlorophenyl)-N- (pyrimidin-2-YL)ACETAMIDE
6ZGV: “Structure of human galactokinase 1 bound with 2-(4-chlorophenyl)-N- (pyrimidin-2-YL)ACETAMIDE”. X-ray diffraction, 3 ligands (HFK, QKZ, GAL), 14 pockets (best druggability 0.84). MolNFT v1 #171795 on GenesisL1: 3D structure, binding…
- PDB
- 6ZGV
- Type
- protein
- Length
- 1,538 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, QKZ, GAL
- Pockets
- 14 · 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 | 42% helix, 23% strand | P51570 |
| B | Galactokinase (EC 2.7.1.6) | protein | 387 | 41% helix, 24% strand | P51570 |
| E | Galactokinase (EC 2.7.1.6) | protein | 391 | 42% helix, 24% strand | P51570 |
| D | Galactokinase (EC 2.7.1.6) | protein | 372 | 44% helix, 26% 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
- QKZ · 2-(4-chlorophenyl)-~{N}-pyrimidin-2-yl-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
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.84 | 0.86 | 79 | empty |
| 2 | 994 | 0.84 | 0.85 | 84 | empty |
| 3 | 1013 | 0.83 | 0.84 | 103 | empty |
| 4 | 434 | 0.78 | 0.87 | 52 | GAL, HFK |
| 5 | 401 | 0.77 | 0.87 | 51 | GAL, HFK |
Interfaces
5 interfaces between chains.
- A–B · 1077 Ų buried · 16 hydrogen bonds · protein-protein
- E–D · 914 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 322 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 268 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 257 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6ZGV · 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 6ZGV · PDBe 6ZGV · UniProt P51570
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