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Fluorine in PDB 7vds: The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24

Enzymatic activity of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24

All present enzymatic activity of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24:
2.7.11.1;

Protein crystallography data

The structure of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24, PDB code: 7vds 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) 48.51 / 3.05
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 118.06, 118.06, 153.69, 90, 90, 120
R / Rfree (%) 22.5 / 27.2

Other elements in 7vds:

The structure of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24 also contains other interesting chemical elements:

Chlorine (Cl) 19 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24 (pdb code 7vds). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24, PDB code: 7vds:

Fluorine binding site 1 out of 1 in 7vds

Go back to Fluorine Binding Sites List in 7vds
Fluorine binding site 1 out of 1 in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24


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 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:123.2
occ:1.00
 F A:61U301 0.0 123.2 1.0
C24 A:61U301 1.3 119.0 1.0
C23 A:61U301 2.3 123.8 1.0
C15 A:61U301 2.4 116.6 1.0
C26 A:61U301 2.8 99.8 1.0
N3 A:61U301 3.0 104.2 1.0
C14 A:61U301 3.0 98.7 1.0
CD2 A:LEU133 3.3 103.2 1.0
C22 A:61U301 3.6 128.4 1.0
C16 A:61U301 3.7 123.2 1.0
O A:HOH441 3.8 104.2 1.0
C27 A:61U301 3.8 91.7 1.0
O A:GLN85 3.9 96.8 1.0
C A:GLN85 3.9 99.5 1.0
N2 A:61U301 4.0 95.3 1.0
N A:ASP86 4.1 99.3 1.0
CG2 A:ILE10 4.1 121.1 1.0
C17 A:61U301 4.2 125.3 1.0
CB A:ASP86 4.2 103.6 1.0
N6 A:61U301 4.4 83.9 1.0
CA A:GLN85 4.5 100.9 1.0
OD2 A:ASP86 4.6 103.5 1.0
CA A:ASP86 4.6 97.0 1.0
CG A:LEU133 4.6 99.3 1.0
C12 A:61U301 4.7 90.9 1.0
CG A:ASP86 4.7 104.3 1.0
C25 A:61U301 4.7 130.9 1.0
C13 A:61U301 4.8 92.3 1.0
O A:CYS83 4.8 113.3 1.0
CD1 A:LEU133 5.0 101.4 1.0

Reference:

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
Page generated: Wed Jul 16 01:12:41 2025

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