Research workbench
Crystal structure of glucokinase (hexokinase 4) complexed with ligand diethyl ({2-[3-(4-methanesulfonylpheno xy)-5-{[(2S)-1-methoxypropan- 2-YL]OXY}BENZAMIDO]-1,3-thiaz ol-4-YL}METHYL)PHOSPHONATE
Analyse Crystal structure of glucokinase (hexokinase 4) complexed with ligand diethyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T78
- Type
- protein
- Length
- 888 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
- G2T, GLC, NA
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 2 of hexokinase-4 (EC 2.7.1.1) | protein | 441 | 43% helix, 21% strand | P35557 |
| B | Isoform 2 of hexokinase-4 (EC 2.7.1.1) | protein | 447 | 45% helix, 21% strand | P35557 |
Ligands and binding sites
- G2T · diethyl {[2-(3-[4-(methanesulfonyl)phenoxy]-5-{[(2S)-1-methoxypropan-2-yl]oxy}benzamido)-1,3-thiazol-4-yl]methyl}phosphonate · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.74 | 0.89 | 47 | EDO |
| 2 | 668 | 0.73 | 0.79 | 74 | empty |
| 3 | 303 | 0.67 | 0.82 | 32 | G2T |
| 4 | 345 | 0.65 | 0.80 | 39 | GLC |
| 5 | 422 | 0.64 | 0.78 | 54 | GLC |
Interfaces
1 interface between chains.
- A–B · 1071 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7T78 · Crystal structure of glucokinase (hexokinase 4) complexed with ligand 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 A 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 7T78 · PDBe 7T78 · UniProt P35557
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