MolNFT v1 · #138037 · protein
Choline kinase alpha in complex with tcd-717
5W6O: “Choline kinase alpha in complex with tcd-717”. X-ray diffraction, 1 ligand (9X1), 9 pockets (best druggability 0.74). MolNFT v1 #138037 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5W6O
- Type
- protein
- Length
- 705 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
- 9X1
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 54% 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 | 352 | 54% helix, 14% strand | P35790 |
| B | Choline kinase alpha (EC 2.7.1.32, 2.7.1.82) | protein | 353 | 54% helix, 14% strand | P35790 |
Ligands and binding sites
- 9X1 · 1,1'-[[1,1'-biphenyl]-4,4'-diylbis(methylene)]bis{4-[(4-chlorophenyl)(methyl)amino]quinolin-1-ium} · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.74 | 0.77 | 76 | 9X1, MES |
| 2 | 885 | 0.74 | 0.78 | 71 | 9X1, MES |
| 3 | 100 | 0.56 | 0.85 | 22 | empty |
| 4 | 97 | 0.55 | 0.84 | 21 | empty |
| 5 | 184 | 0.53 | 0.78 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1307 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
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 5W6O · PDBe 5W6O · UniProt P35790
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