MolNFT v1 · #172362 · protein

Structure of human CKA1 in complex with compound B

7A04 · Choline kinase alpha: “Structure of human CKA1 in complex with compound B”. X-ray diffraction, 1 ligand (QTK), 10 pockets (best druggability 0.60). MolNFT v1 #172362 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7A04
Type: protein
Length: 696 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: QTK
Pockets: 10 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Choline kinase alpha (EC 2.7.1.32, 2.7.1.82)	protein	348	53% helix, 14% strand	P35790

Ligands and binding sites

QTK · 1-(phenylmethyl)-4-pyrrolidin-1-yl-pyridin-1-ium · ligand · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 5 copies · chains A, 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	421	0.60	0.76	34	QTK
2	389	0.59	0.76	33	QTK, EDO
3	142	0.57	0.83	25	empty
4	93	0.57	0.86	22	empty
5	172	0.48	0.76	28	empty

Interfaces

1 interface between chains.

A–B · 1078 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

7A04 · Structure of human CKa1 in complex with compound b · 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 7A04 · PDBe 7A04 · UniProt P35790

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