Fluorine in PDB 7vdu: The Structure of Cyclin-Dependent Kinase 2 (CDK2) in Complex with Compound 1

All present enzymatic activity of The Structure of Cyclin-Dependent Kinase 2 (CDK2) in Complex with Compound 1:
2.7.11.22;

The structure of The Structure of Cyclin-Dependent Kinase 2 (CDK2) in Complex with Compound 1, PDB code: 7vdu was solved by G.Malojcic, S.L.Clugston, M.Daniels, J.C.Harmange, M.Ledeborer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.81 / 1.53
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.851, 73.035, 70.731, 90, 90, 90
R / Rfree (%)	17.6 / 21.8

The binding sites of Fluorine atom in the The Structure of Cyclin-Dependent Kinase 2 (CDK2) in Complex with Compound 1 (pdb code 7vdu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the The Structure of Cyclin-Dependent Kinase 2 (CDK2) in Complex with Compound 1, PDB code: 7vdu:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the The Structure of Cyclin-Dependent Kinase 2 (CDK2) in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Structure of Cyclin-Dependent Kinase 2 (CDK2) in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:25.5 occ:0.50 F31 A:65L301 0.0 25.5 0.5 C10 A:65L301 1.3 28.2 0.5 C30 A:65L301 1.3 27.2 0.5 C9 A:65L301 2.3 27.4 0.5 C32 A:65L301 2.3 26.6 0.5 C11 A:65L301 2.4 25.6 1.0 N12 A:65L301 2.8 23.4 1.0 C14 A:65L301 3.0 21.0 1.0 C13 A:65L301 3.1 20.8 1.0 CD2 A:LEU134 3.5 19.9 1.0 C A:GLN85 3.5 21.2 1.0 N A:ASP86 3.6 21.5 1.0 C8 A:65L301 3.6 32.8 1.0 C30 A:65L301 3.6 29.7 0.5 C10 A:65L301 3.6 28.6 0.5 CA A:GLN85 3.7 21.6 1.0 O A:HOH581 3.8 40.6 1.0 O A:GLN85 3.9 20.9 1.0 C15 A:65L301 4.1 17.6 1.0 C9 A:65L301 4.1 31.4 0.5 C32 A:65L301 4.1 31.2 0.5 O A:HOH409 4.1 24.6 1.0 CB A:ASP86 4.2 23.9 1.0 N29 A:65L301 4.2 20.3 1.0 CA A:ASP86 4.3 21.5 1.0 N A:GLN85 4.3 21.4 1.0 CD1 A:LEU134 4.4 19.5 1.0 CG A:LEU134 4.4 18.7 1.0 O A:HOH441 4.5 33.7 1.0 N16 A:65L301 4.7 20.6 1.0 CG2 A:ILE10 4.7 31.7 1.0 N6 A:65L301 4.7 38.1 1.0 F31 A:65L301 4.7 37.7 0.5 CG A:ASP86 4.8 28.9 1.0 O A:LEU83 4.8 23.4 1.0 OD2 A:ASP86 4.8 28.2 1.0 C A:HIS84 4.9 21.3 1.0 CB A:LEU134 4.9 16.7 1.0 O A:HIS84 4.9 23.8 1.0

Fluorine binding site 2 out of 2 in the The Structure of Cyclin-Dependent Kinase 2 (CDK2) in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Structure of Cyclin-Dependent Kinase 2 (CDK2) in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:37.7 occ:0.50 F31 A:65L301 0.0 37.7 0.5 C10 A:65L301 1.3 28.6 0.5 C30 A:65L301 1.3 29.7 0.5 C9 A:65L301 2.3 31.4 0.5 C32 A:65L301 2.3 31.2 0.5 C11 A:65L301 2.4 25.6 1.0 N12 A:65L301 2.8 23.4 1.0 CE1 A:PHE82 2.9 22.9 1.0 CZ A:PHE82 3.0 25.2 1.0 C8 A:65L301 3.5 32.8 1.0 C30 A:65L301 3.6 27.2 0.5 C10 A:65L301 3.6 28.2 0.5 O A:LEU83 3.6 23.4 1.0 CG1 A:ILE10 3.7 26.7 1.0 CD1 A:ILE10 3.8 24.9 1.0 C13 A:65L301 3.9 20.8 1.0 CD1 A:PHE82 4.0 21.9 1.0 O A:HIS84 4.0 23.8 1.0 C32 A:65L301 4.0 26.6 0.5 C9 A:65L301 4.0 27.4 0.5 CE2 A:PHE82 4.2 26.8 1.0 CG2 A:ILE10 4.5 31.7 1.0 C14 A:65L301 4.7 21.0 1.0 C A:HIS84 4.7 21.3 1.0 N6 A:65L301 4.7 38.1 1.0 CB A:ILE10 4.7 29.7 1.0 N29 A:65L301 4.7 20.3 1.0 O A:HOH468 4.7 29.5 1.0 F31 A:65L301 4.7 25.5 0.5 C A:LEU83 4.8 19.1 1.0 CG A:PHE82 5.0 21.1 1.0

M.H.Daniels, G.Malojcic, S.L.Clugston, B.Williams, M.Coeffet-Le Gal, X.R.Pan-Zhou, S.Venkatachalan, J.C.Harmange, M.Ledeboer. Discovery and Optimization of Highly Selective Inhibitors of CDK5. J.Med.Chem. V. 65 3575 2022.
ISSN: ISSN 0022-2623
PubMed: 35143203
DOI: 10.1021/ACS.JMEDCHEM.1C02069