MolNFT v1 · #188006 · protein
Crystal structure of glucokinase (hexokinase 4) complexed with ligand aka diethyl {[3-(3-{[5-(azetidine-1-carbon YL)PYRAZIN-2-YL]OXY}-5- (propan-2-YLOXY)BENZAMIDO)-1H- pyrazol-1-YL]METHYL}PHOSPHONATE
7T79 · Isoform 2 of hexokinase-4: “Crystal structure of glucokinase (hexokinase 4) complexed with ligand aka diethyl…”. X-ray diffraction, 2 ligands (G1S, GLC), 8 pockets (best druggability 0.79). MolNFT v1 #188006 on GenesisL1: 3D…
- PDB
- 7T79
- Type
- protein
- Length
- 889 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2 of hexokinase-4
- EC
- 2.7.1.1
- UniProt
- P35557
- Ligands
- G1S, GLC
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 2 of hexokinase-4 (EC 2.7.1.1) | protein | 445 | 46% helix, 21% strand | P35557 |
| B | Isoform 2 of hexokinase-4 (EC 2.7.1.1) | protein | 444 | 45% helix, 22% strand | P35557 |
Ligands and binding sites
- G1S · diethyl {[3-(3-{[5-(azetidine-1-carbonyl)pyrazin-2-yl]oxy}-5-[(propan-2-yl)oxy]benzamido)-1H-pyrazol-1-yl]methyl}phosphonate · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.79 | 0.84 | 93 | GLC |
| 2 | 233 | 0.68 | 0.85 | 28 | G1S |
| 3 | 251 | 0.68 | 0.84 | 26 | G1S |
| 4 | 455 | 0.64 | 0.77 | 62 | GLC |
| 5 | 137 | 0.46 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 937 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7T79 · Crystal structure of glucokinase (hexokinase 4) complexed with ligand aka diethyl… · the same entry in another collection · chain A against A, TM-score 1.00
- P35557 · AlphaFold monomer V2.0 prediction for hexokinase-4 (P35557) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 7T79 · PDBe 7T79 · UniProt P35557
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