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Crystal structure of choline kinase alpha-1 bound by 5-[(4-methyl-1,4- diazepan-1-YL)METHYL]-2-[4-[(4-methyl-1,4-diazepan-1-yl) METHYL]PHENYL]BENZENECARBONITRILE (compound 65)

Analyse Crystal structure of choline kinase alpha-1 bound by 5-[(4-methyl-1,4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5EQY
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: 5RA
Pockets: 7 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Choline kinase alpha (EC 2.7.1.32, 2.7.1.82)	protein	352	50% helix, 14% strand	P35790
B	Choline kinase alpha (EC 2.7.1.32, 2.7.1.82)	protein	351	52% helix, 15% strand	P35790

Ligands and binding sites

5RA · 5-[(4-methyl-1,4-diazepan-1-yl)methyl]-2-[4-[(4-methyl-1,4-diazepan-1-yl)methyl]phenyl]benzenecarbonitrile · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	820	0.69	0.75	66	5RA
2	489	0.64	0.76	41	5RA
3	85	0.59	0.87	22	empty
4	88	0.55	0.85	21	empty
5	233	0.53	0.76	31	empty

Interfaces

1 interface between chains.

A–B · 1240 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

5EQY · Crystal structure of choline kinase alpha-1 bound by… · 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 5EQY · PDBe 5EQY · UniProt P35790

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