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Crystal structure of human hexokinase 2 with cmpd 27, a 2-amido-6- benzenesulfonamide glucosamine
Analyse Crystal structure of human hexokinase 2 with cmpd 27, a 2-amido-6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HFU
- Type
- protein
- Length
- 1,792 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hexokinase-2
- EC
- 2.7.1.1
- UniProt
- P52789
- Ligands
- 603
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hexokinase-2 (EC 2.7.1.1) | protein | 895 | 46% helix, 19% strand | P52789 |
| B | Hexokinase-2 (EC 2.7.1.1) | protein | 897 | 44% helix, 20% strand | P52789 |
Ligands and binding sites
- 603 · ~{N}-[(2~{S},3~{R},4~{R},5~{S},6~{R})-6-[[(4-cyanophenyl)sulfonylamino]methyl]-2,4,5-tris(oxidanyl)oxan-3-yl]-3-phenyl-benzamide · ligand · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.75 | 0.79 | 83 | empty |
| 2 | 552 | 0.72 | 0.81 | 52 | empty |
| 3 | 427 | 0.67 | 0.80 | 47 | empty |
| 4 | 589 | 0.66 | 0.76 | 67 | 603 |
| 5 | 502 | 0.64 | 0.77 | 63 | 603 |
Interfaces
1 interface between chains.
- A–B · 756 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5HFU · Crystal Structure of Human Hexokinase 2 with cmpd 27, a 2-amido-6-benzenesulfonamide… · 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 B against A, TM-score 0.82
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 5HFU · PDBe 5HFU · UniProt P52789
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