Fluorine in PDB 7vdr: The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 13

All present enzymatic activity of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 13:
2.7.11.1;

The structure of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 13, PDB code: 7vdr 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)	29.65 / 2.55
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.83, 117.83, 154.93, 90, 90, 120
R / Rfree (%)	21.9 / 25.6

The binding sites of Fluorine atom in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 13 (pdb code 7vdr). 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 13, PDB code: 7vdr:
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 13


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 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:55.1 occ:1.00 F25 A:63I301 0.0 55.1 1.0 C24 A:63I301 1.3 52.0 1.0 C19 A:63I301 2.3 54.2 1.0 C23 A:63I301 2.4 51.9 1.0 N18 A:63I301 2.7 49.4 1.0 O A:CYS83 3.3 56.7 1.0 CE2 A:PHE82 3.4 58.0 1.0 CZ A:PHE82 3.5 58.9 1.0 CG1 A:ILE10 3.5 75.2 1.0 O A:ASP84 3.6 54.9 1.0 C20 A:63I301 3.6 54.2 1.0 C22 A:63I301 3.6 56.7 1.0 CD1 A:ILE10 3.8 72.7 1.0 CG2 A:ILE10 3.8 80.3 1.0 C17 A:63I301 4.0 47.7 1.0 C21 A:63I301 4.1 55.8 1.0 C A:ASP84 4.1 52.4 1.0 CB A:ILE10 4.3 77.2 1.0 C A:CYS83 4.5 54.5 1.0 CD2 A:PHE82 4.5 55.6 1.0 N A:GLN85 4.6 50.5 1.0 CE1 A:PHE82 4.6 59.2 1.0 CA A:GLN85 4.8 52.3 1.0 N16 A:63I301 4.8 45.9 1.0 N26 A:63I301 4.8 60.5 1.0 C31 A:63I301 4.8 45.0 1.0 CA A:ASP84 4.8 55.4 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 13


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 13 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:92.2 occ:1.00 F25 B:63I301 0.0 92.2 1.0 C24 B:63I301 1.3 95.6 1.0 C19 B:63I301 2.4 95.8 1.0 C23 B:63I301 2.4 94.6 1.0 N18 B:63I301 2.7 90.8 1.0 CE2 B:PHE82 3.1 94.5 1.0 CG1 B:ILE10 3.5 110.0 1.0 CZ B:PHE82 3.5 94.5 1.0 CD1 B:ILE10 3.5 110.5 1.0 O B:CYS83 3.5 83.8 1.0 C20 B:63I301 3.6 95.2 1.0 C22 B:63I301 3.6 91.9 1.0 C17 B:63I301 3.9 89.5 1.0 CG2 B:ILE10 4.1 105.6 1.0 C21 B:63I301 4.1 92.4 1.0 CD2 B:PHE82 4.1 94.8 1.0 O B:ASP84 4.2 89.0 1.0 CB B:ILE10 4.4 107.3 1.0 C B:ASP84 4.7 86.5 1.0 CE1 B:PHE82 4.7 95.7 1.0 C31 B:63I301 4.7 88.5 1.0 N16 B:63I301 4.7 89.8 1.0 C B:CYS83 4.7 85.2 1.0 N26 B:63I301 4.8 85.1 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