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Structure of cyclin-dependent kinase 2 with small-molecule ligand 3- (4,7-dichloro-1H-indol-3-YL)PROP-2-yn-1-ol (AT17833) in an alternate binding site.

Analyse Structure of cyclin-dependent kinase 2 with small-molecule ligand 3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5FP6
Type: protein
Length: 278 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclin-dependent kinase 2
EC: 2.7.11.22
UniProt: P24941
Ligands: MFZ
Pockets: 1 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclin-dependent kinase 2 (EC 2.7.11.22)	protein	278	37% helix, 18% strand	P24941

Ligands and binding sites

MFZ · 3-(4,7-dichloro-1H-indol-3-yl)prop-2-yn-1-ol · ligand · 2 copies · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	480	0.71	0.81	67	MFZ

Compared structures

5FP6 · Structure of cyclin-dependent kinase 2 with small-molecule ligand… · the same entry in another collection · chain A against A, TM-score 1.00
P24941 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 2 (P24941) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P24941
Elsewhere: RCSB PDB 5FP6 · PDBe 5FP6 · UniProt P24941

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