Research workbench
Crystal structure of human hexokinase 2 with cmpd 1, a C-2-substituted glucosamine
Analyse Crystal structure of human hexokinase 2 with cmpd 1, a C-2-substituted… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HG1
- Type
- protein
- Length
- 867 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hexokinase-2
- EC
- 2.7.1.1
- UniProt
- P52789
- Ligands
- 62C, BG6
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hexokinase-2 (EC 2.7.1.1) | protein | 867 | 45% helix, 17% strand | P52789 |
Ligands and binding sites
- 62C · 2-deoxy-2-{[(2E)-3-(3,4-dichlorophenyl)prop-2-enoyl]amino}-alpha-D-glucopyranose · ligand · 2 copies · chains A
- BG6 · 6-O-phosphono-beta-D-glucopyranose · sugar · chains A
- FLC · Citrate anion · additive · chains A
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 | 459 | 0.72 | 0.81 | 37 | empty |
| 2 | 653 | 0.71 | 0.79 | 65 | empty |
| 3 | 509 | 0.71 | 0.80 | 63 | 62C, BG6, FLC |
| 4 | 457 | 0.65 | 0.78 | 58 | 62C |
| 5 | 99 | 0.41 | 0.77 | 17 | empty |
Modifications
Observed in the structure: 1 glycan (O-glycosylation).
Compared structures
- 5HG1 · Crystal Structure of Human Hexokinase 2 with cmpd 1, a C-2-substituted glucosamine · the same entry in another collection · chain A against A, TM-score 1.00
- P52789 · AlphaFold monomer V2.0 prediction for hexokinase-2 (P52789) · a predicted model of the same protein · chain A against A, TM-score 0.86
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 P52789
- Elsewhere: RCSB PDB 5HG1 · PDBe 5HG1 · UniProt P52789
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