MolNFT v1 · #82193 · protein
Glucokinase in complex with glucose and activator
3VF6: “Glucokinase in complex with glucose and activator”. X-ray diffraction, 3 ligands (0H6, GLC, NA), 4 pockets (best druggability 0.59). MolNFT v1 #82193 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VF6
- Type
- protein
- Length
- 451 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucokinase
- EC
- 2.7.1.2
- UniProt
- P35557
- Ligands
- 0H6, GLC, NA
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucokinase (EC 2.7.1.2) | protein | 451 | 46% helix, 21% strand | P35557 |
Ligands and binding sites
- 0H6 · 6-({(2S)-3-cyclopentyl-2-[4-(trifluoromethyl)-1H-imidazol-1-yl]propanoyl}amino)pyridine-3-carboxylic acid · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.59 | 0.79 | 29 | 0H6 |
| 2 | 234 | 0.59 | 0.80 | 30 | GLC |
| 3 | 167 | 0.45 | 0.75 | 34 | empty |
| 4 | 64 | 0.36 | 0.78 | 14 | empty |
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 P35557
- Elsewhere: RCSB PDB 3VF6 · PDBe 3VF6 · UniProt P35557
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