MolNFT v1 · #118050 · protein
Crystal structure of choline kinase alpha-1 bound by [4-[(4-methyl-1, 4-diazepan-1-YL)METHYL]PHENYL]METHANAMINE (compound 11)
5EQE: “Crystal structure of choline kinase alpha-1 bound by [4-[(4-methyl-1…”. X-ray diffraction, 1 ligand (5R8), 6 pockets (best druggability 0.73). MolNFT v1 #118050 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5EQE
- Type
- protein
- Length
- 697 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
- 5R8
- Pockets
- 6 · best druggability 0.73
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 | 353 | 52% helix, 14% strand | P35790 |
| B | Choline kinase alpha (EC 2.7.1.32, 2.7.1.82) | protein | 344 | 51% helix, 15% strand | P35790 |
Ligands and binding sites
- 5R8 · [4-[(4-methyl-1,4-diazepan-1-yl)methyl]phenyl]methanamine · ligand · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.73 | 0.76 | 76 | 5R8 |
| 2 | 522 | 0.69 | 0.79 | 55 | 5R8 |
| 3 | 192 | 0.51 | 0.77 | 29 | empty |
| 4 | 185 | 0.50 | 0.77 | 28 | empty |
| 5 | 178 | 0.48 | 0.76 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1168 Ų buried · 17 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 5EQE · PDBe 5EQE · UniProt P35790
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