MolNFT v1 · #87113 · protein
Determination of potential scaffolds for human choline kinase alpha 1 by chemical deconvolution studies
4BR3: “Determination of potential scaffolds for human choline kinase alpha 1 by chemical deconvolution studies”. X-ray diffraction, 3 ligands (U85, A4V, PO4), 10 pockets (best druggability 0.75). MolNFT v1 #87113 on GenesisL1: 3D…
- PDB
- 4BR3
- Type
- protein
- Length
- 703 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Choline kinase alpha
- EC
- 2.7.1.32, 2.7.1.82
- UniProt
- P35790
- Ligands
- U85, A4V, PO4
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Choline kinase alpha (EC 2.7.1.32, 2.7.1.82) | protein | 354 | 52% helix, 14% strand | P35790 |
| B | Choline kinase alpha (EC 2.7.1.32, 2.7.1.82) | protein | 349 | 52% helix, 14% strand | P35790 |
Ligands and binding sites
- U85 · 1-((4'-((6-amino-3H-purin-3-yl)methyl)biphenyl-4-yl)methyl)-4-(dimethylamino)pyridinium · ligand · 2 copies · chains A, B
- A4V · 3-benzyladenine · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.75 | 0.78 | 80 | U85, A4V |
| 2 | 811 | 0.70 | 0.76 | 61 | U85 |
| 3 | 131 | 0.64 | 0.87 | 29 | A4V |
| 4 | 187 | 0.51 | 0.77 | 30 | empty |
| 5 | 83 | 0.45 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1289 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4BR3 · Determination of potential scaffolds for human choline kinase alpha 1 by chemical… · 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 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 P35790
- Elsewhere: RCSB PDB 4BR3 · PDBe 4BR3 · UniProt P35790
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