MolNFT v2 · #63212 · protein
Crystal structure of human choline kinase alpha in complex with hemicholinium-3
3F2R: “Crystal structure of human choline kinase alpha in complex with hemicholinium-3”. X-ray diffraction at 2.35, 2 ligands (HC6, UNX), 6 pockets (best druggability 0.69). MolNFT v2 #63212 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3F2R
- Type
- protein
- Length
- 654 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.35
- Source
- Homo sapiens
- Molecule
- Choline kinase alpha
- EC
- 2.7.1.32
- UniProt
- P35790
- Ligands
- HC6, UNX
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · resolution 2.35 · 2 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Choline kinase alpha (EC 2.7.1.32) | protein | 348 | 53% helix, 14% strand | P35790 |
| B | Choline kinase alpha (EC 2.7.1.32) | protein | 306 | 53% helix, 13% strand | P35790 |
Ligands and binding sites
- HC6 · (2S,2'S)-2,2'-biphenyl-4,4'-diylbis(2-hydroxy-4,4-dimethylmorpholin-4-ium) · ligand · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.69 | 0.78 | 54 | HC6 |
| 2 | 521 | 0.65 | 0.76 | 69 | HC6 |
| 3 | 182 | 0.50 | 0.77 | 30 | empty |
| 4 | 190 | 0.47 | 0.75 | 25 | empty |
| 5 | 75 | 0.36 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1060 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3F2R · Crystal structure of human choline kinase alpha in complex with hemicholinium-3 · the same entry in another collection · chain A against A, TM-score 1.00
- P35790 · AlphaFold monomer V2.0 prediction for choline kinase alpha (P35790) · 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 P35790
- Elsewhere: RCSB PDB 3F2R · PDBe 3F2R · UniProt P35790
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