Fluorine in PDB 7vdp: The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 1

All present enzymatic activity of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 1:
2.7.11.1;

The structure of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 1, PDB code: 7vdp 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)	51.79 / 2.09
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	118.37, 118.37, 155.37, 90, 90, 120
R / Rfree (%)	20.1 / 22.9

The structure of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 1 also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Fluorine atom in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 1 (pdb code 7vdp). 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 1, PDB code: 7vdp:
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 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 5 (CDK5) in Complex with P25 and Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:45.1 occ:1.00 F31 A:65L301 0.0 45.1 1.0 C30 A:65L301 1.3 42.1 1.0 C32 A:65L301 2.3 41.8 1.0 C11 A:65L301 2.4 40.5 1.0 N12 A:65L301 2.7 37.5 1.0 O A:CYS83 3.3 36.4 1.0 O A:HOH562 3.3 71.8 1.0 O A:ASP84 3.3 38.0 1.0 CE2 A:PHE82 3.3 43.4 1.0 O A:HOH421 3.5 51.6 1.0 CZ A:PHE82 3.5 44.9 1.0 CD1 A:ILE10 3.6 54.4 1.0 C10 A:65L301 3.6 40.6 1.0 C8 A:65L301 3.6 45.4 1.0 CG1 A:ILE10 3.6 55.8 1.0 C A:ASP84 3.9 38.8 1.0 C13 A:65L301 3.9 35.0 1.0 CG2 A:ILE10 4.0 59.3 1.0 C9 A:65L301 4.1 44.4 1.0 CD2 A:PHE82 4.4 42.3 1.0 CB A:ILE10 4.4 57.6 1.0 C A:CYS83 4.4 36.2 1.0 N A:GLN85 4.5 36.9 1.0 CA A:ASP84 4.6 39.7 1.0 O A:HOH527 4.7 58.8 1.0 N29 A:65L301 4.7 34.1 1.0 CE1 A:PHE82 4.7 45.3 1.0 CA A:GLN85 4.7 38.5 1.0 C14 A:65L301 4.8 32.2 1.0 N6 A:65L301 4.8 49.8 1.0 N A:ASP84 5.0 36.9 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 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 5 (CDK5) in Complex with P25 and Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:72.5 occ:1.00 F31 B:65L301 0.0 72.5 1.0 C30 B:65L301 1.3 75.2 1.0 C32 B:65L301 2.4 73.9 1.0 C11 B:65L301 2.4 76.1 1.0 N12 B:65L301 2.8 74.2 1.0 CE2 B:PHE82 3.2 86.7 1.0 CD1 B:ILE10 3.2 104.6 1.0 CG1 B:ILE10 3.4 105.7 1.0 CZ B:PHE82 3.5 86.9 1.0 C10 B:65L301 3.6 74.6 1.0 C8 B:65L301 3.6 73.0 1.0 O B:CYS83 3.6 72.3 1.0 C13 B:65L301 3.8 74.8 1.0 O B:ASP84 3.9 67.8 1.0 CG2 B:ILE10 4.0 103.2 1.0 C9 B:65L301 4.1 73.5 1.0 CD2 B:PHE82 4.3 87.8 1.0 CB B:ILE10 4.3 104.6 1.0 C B:ASP84 4.5 69.1 1.0 N29 B:65L301 4.5 74.9 1.0 C14 B:65L301 4.6 73.0 1.0 CE1 B:PHE82 4.8 89.2 1.0 N6 B:65L301 4.8 70.1 1.0 C B:CYS83 4.8 73.4 1.0 N B:GLN85 5.0 65.4 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