Fluorine in PDB 7vdq: The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 7

All present enzymatic activity of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 7:
2.7.11.1;

The structure of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 7, PDB code: 7vdq 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)	38.50 / 2.91
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.61, 117.61, 154.01, 90, 90, 120
R / Rfree (%)	25.2 / 28.4

The binding sites of Fluorine atom in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 7 (pdb code 7vdq). 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 5 (CDK5) in Complex with P25 and Compound 7, PDB code: 7vdq:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 7


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 5 (CDK5) in Complex with P25 and Compound 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:69.5 occ:1.00 F23 A:64V301 0.0 69.5 1.0 C22 A:64V301 1.3 64.6 1.0 C21 A:64V301 2.3 65.4 1.0 C24 A:64V301 2.4 63.7 1.0 N20 A:64V301 2.7 64.1 1.0 CE2 A:PHE82 3.1 65.4 1.0 O A:CYS83 3.1 66.2 1.0 CZ A:PHE82 3.5 66.8 1.0 O A:ASP84 3.5 61.9 1.0 CG1 A:ILE10 3.5 79.7 1.0 C27 A:64V301 3.6 65.0 1.0 C25 A:64V301 3.6 66.4 1.0 CD1 A:ILE10 3.6 78.8 1.0 C19 A:64V301 3.9 60.6 1.0 CG2 A:ILE10 4.0 82.8 1.0 C A:ASP84 4.0 63.4 1.0 C26 A:64V301 4.1 64.9 1.0 CD2 A:PHE82 4.1 64.5 1.0 C A:CYS83 4.3 63.5 1.0 CB A:ILE10 4.4 81.1 1.0 N A:GLN85 4.6 62.4 1.0 N18 A:64V301 4.7 60.9 1.0 CA A:ASP84 4.7 65.6 1.0 CE1 A:PHE82 4.7 66.9 1.0 C35 A:64V301 4.8 59.6 1.0 N28 A:64V301 4.8 72.0 1.0 CA A:GLN85 4.9 63.3 1.0 N A:ASP84 4.9 63.6 1.0

Fluorine binding site 2 out of 2 in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 7


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 5 (CDK5) in Complex with P25 and Compound 7 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:104.0 occ:1.00 F23 B:64V301 0.0 104.0 1.0 C22 B:64V301 1.4 103.6 1.0 C21 B:64V301 2.4 102.4 1.0 C24 B:64V301 2.4 103.2 1.0 N20 B:64V301 2.8 96.4 1.0 C19 B:64V301 3.6 90.5 1.0 C27 B:64V301 3.6 108.2 1.0 C25 B:64V301 3.7 106.5 1.0 CE2 B:PHE82 3.8 113.3 1.0 C26 B:64V301 4.1 106.5 1.0 C35 B:64V301 4.2 92.5 1.0 O B:CYS83 4.3 104.0 1.0 N18 B:64V301 4.4 89.7 1.0 CD2 B:PHE82 4.5 113.9 1.0 CZ B:PHE82 4.6 113.6 1.0 N28 B:64V301 4.8 106.8 1.0 O B:ASP84 4.9 109.0 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