Research workbench
Structure of khk in complex with compound 8 (2-[(1~{S},5~{R})-3-[2- [(2~{S})-2-methylazetidin-1-yl]-6-(TRIFLUOROMETHYL)PYRIMIDIN-4-yl]-3- AZABICYCLO[3.1.0]HEXAN-6-YL]ETHANOIC acid)
Analyse Structure of khk in complex with compound 8 (2-[(1~{S},5~{R})-3-[2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W0Z
- Type
- protein
- Length
- 597 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ketohexokinase
- EC
- 2.7.1.3
- UniProt
- P50053
- Ligands
- S6D, SO4
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ketohexokinase (EC 2.7.1.3) | protein | 296 | 36% helix, 25% strand | P50053 |
| B | Ketohexokinase (EC 2.7.1.3) | protein | 301 | 35% helix, 25% strand | P50053 |
Ligands and binding sites
- S6D · 2-[(1~{S},5~{R})-3-[2-[(2~{S})-2-methylazetidin-1-yl]-6-(trifluoromethyl)pyrimidin-4-yl]-3-azabicyclo[3.1.0]hexan-6-yl]ethanoic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
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 | 951 | 0.77 | 0.79 | 109 | S6D, SO4 |
| 2 | 684 | 0.76 | 0.82 | 66 | S6D |
| 3 | 79 | 0.36 | 0.76 | 19 | empty |
| 4 | 51 | 0.31 | 0.77 | 14 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1767 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 6W0Z · Structure of KHK in complex with compound 8 (2-[(1~{S},5~{R})-3-[2-[(2~{S})-2-methylazetid… · the same entry in another collection · chain A against A, TM-score 1.00
- P50053 · AlphaFold monomer V2.0 prediction for ketohexokinase (P50053) · 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 P50053
- Elsewhere: RCSB PDB 6W0Z · PDBe 6W0Z · UniProt P50053
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