Fluorine in PDB 5hvy: CDK8/Cycc in Complex with Compound 20

All present enzymatic activity of CDK8/Cycc in Complex with Compound 20:
2.7.11.22; 2.7.11.23;

The structure of CDK8/Cycc in Complex with Compound 20, PDB code: 5hvy was solved by J.R.Kiefer, E.V.Schneider, K.Maskos, P.Bergeron, M.Koehler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.27 / 2.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.184, 71.859, 180.821, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 22

The structure of CDK8/Cycc in Complex with Compound 20 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the CDK8/Cycc in Complex with Compound 20 (pdb code 5hvy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the CDK8/Cycc in Complex with Compound 20, PDB code: 5hvy:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the CDK8/Cycc in Complex with Compound 20


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of CDK8/Cycc in Complex with Compound 20 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:37.7 occ:1.00 F33 A:66X501 0.0 37.7 1.0 C32 A:66X501 1.3 37.3 1.0 F35 A:66X501 2.1 37.6 1.0 F34 A:66X501 2.2 38.4 1.0 C30 A:66X501 2.3 31.8 1.0 H29 A:66X501 2.3 30.2 1.0 HG22 A:ILE79 2.6 42.8 1.0 HA A:ALA172 2.6 35.4 1.0 C31 A:66X501 2.6 25.2 1.0 HG13 A:VAL78 3.1 25.4 1.0 O A:ILE171 3.2 25.4 1.0 HG22 A:ILE171 3.4 27.6 1.0 CG2 A:ILE79 3.5 35.7 1.0 CA A:ALA172 3.5 29.5 1.0 C22 A:66X501 3.6 42.1 1.0 HG21 A:ILE79 3.6 42.8 1.0 HG12 A:VAL78 3.7 25.4 1.0 CG1 A:VAL78 3.8 21.1 1.0 C A:ILE171 3.8 22.1 1.0 H A:ILE79 3.8 31.6 1.0 HG23 A:ILE79 3.8 42.8 1.0 HD21 A:LEU70 3.8 54.4 1.0 N A:ALA172 3.9 31.5 1.0 H18 A:66X501 3.9 43.2 1.0 C A:ALA172 3.9 24.6 1.0 H A:ASP173 4.0 29.3 1.0 C19 A:66X501 4.0 25.3 1.0 HG11 A:VAL78 4.1 25.4 1.0 C23 A:66X501 4.2 36.0 1.0 H19 A:66X501 4.2 43.2 1.0 N A:ASP173 4.2 24.4 1.0 CG2 A:ILE171 4.4 23.0 1.0 O17 A:66X501 4.5 23.6 1.0 N A:ILE79 4.5 26.4 1.0 HD11 A:LEU142 4.5 35.3 1.0 HB A:ILE171 4.5 31.1 1.0 H A:ALA172 4.5 37.8 1.0 HB A:ILE79 4.6 37.2 1.0 CB A:ILE79 4.6 31.0 1.0 O A:ALA172 4.6 27.4 1.0 CB A:ALA172 4.7 28.5 1.0 O A:ILE79 4.7 30.5 1.0 HE2 A:HIS149 4.7 35.2 1.0 CD2 A:LEU70 4.7 45.3 1.0 C21 A:66X501 4.7 29.1 1.0 HD2 A:HIS149 4.7 34.0 1.0 HB2 A:ASP173 4.7 38.9 1.0 HG21 A:ILE171 4.7 27.6 1.0 HD23 A:LEU70 4.7 54.4 1.0 HA A:VAL78 4.8 34.3 1.0 HB2 A:ALA172 4.8 34.2 1.0 HB1 A:ALA172 4.8 34.2 1.0 CB A:ILE171 4.8 26.0 1.0 C20 A:66X501 4.9 37.8 1.0 CA A:ILE171 4.9 23.0 1.0 HG23 A:ILE171 5.0 27.6 1.0

Fluorine binding site 2 out of 3 in the CDK8/Cycc in Complex with Compound 20


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of CDK8/Cycc in Complex with Compound 20 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:38.4 occ:1.00 F34 A:66X501 0.0 38.4 1.0 C32 A:66X501 1.3 37.3 1.0 F33 A:66X501 2.2 37.7 1.0 F35 A:66X501 2.2 37.6 1.0 C30 A:66X501 2.3 31.8 1.0 H19 A:66X501 2.4 43.2 1.0 H18 A:66X501 2.7 43.2 1.0 C23 A:66X501 2.8 36.0 1.0 C22 A:66X501 2.8 42.1 1.0 HD2 A:HIS149 3.0 34.0 1.0 HG22 A:ILE171 3.2 27.6 1.0 HE2 A:HIS149 3.3 35.2 1.0 C31 A:66X501 3.4 25.2 1.0 CD2 A:HIS149 3.4 28.4 1.0 NE2 A:HIS149 3.6 29.3 1.0 HB2 A:ASP173 3.6 38.9 1.0 H29 A:66X501 3.7 30.2 1.0 HA A:ALA172 3.8 35.4 1.0 HD11 A:LEU142 3.8 35.3 1.0 C A:ALA172 4.0 24.6 1.0 CG2 A:ILE171 4.1 23.0 1.0 C21 A:66X501 4.1 29.1 1.0 HG21 A:ILE171 4.1 27.6 1.0 O A:ALA172 4.1 27.4 1.0 N24 A:66X501 4.2 44.9 1.0 HD13 A:LEU142 4.2 35.3 1.0 CA A:ALA172 4.2 29.5 1.0 N A:ASP173 4.3 24.4 1.0 HG13 A:VAL78 4.3 25.4 1.0 H A:ASP173 4.4 29.3 1.0 CD1 A:LEU142 4.5 29.4 1.0 CB A:ASP173 4.5 32.4 1.0 CG A:HIS149 4.5 25.7 1.0 N A:ALA172 4.5 31.5 1.0 HG23 A:ILE171 4.5 27.6 1.0 C19 A:66X501 4.5 25.3 1.0 H22 A:66X501 4.6 61.3 1.0 H21 A:66X501 4.6 61.3 1.0 HB3 A:ASP173 4.7 38.9 1.0 CE1 A:HIS149 4.7 29.6 1.0 O A:ILE171 4.7 25.4 1.0 C A:ILE171 4.7 22.1 1.0 HG22 A:ILE79 4.7 42.8 1.0 C25 A:66X501 4.7 51.1 1.0 C20 A:66X501 4.8 37.8 1.0 H A:ALA172 4.8 37.8 1.0 HA A:HIS149 4.8 26.3 1.0 H17 A:66X501 4.8 34.9 1.0 H27 A:66X501 4.9 61.8 1.0 HD12 A:LEU142 4.9 35.3 1.0 CA A:ASP173 4.9 32.4 1.0 HD21 A:LEU142 5.0 22.9 1.0 C29 A:66X501 5.0 51.5 1.0

Fluorine binding site 3 out of 3 in the CDK8/Cycc in Complex with Compound 20


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of CDK8/Cycc in Complex with Compound 20 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:37.6 occ:1.00 F35 A:66X501 0.0 37.6 1.0 C32 A:66X501 1.3 37.3 1.0 F33 A:66X501 2.1 37.7 1.0 F34 A:66X501 2.2 38.4 1.0 H18 A:66X501 2.2 43.2 1.0 C30 A:66X501 2.3 31.8 1.0 C23 A:66X501 2.9 36.0 1.0 C22 A:66X501 2.9 42.1 1.0 H19 A:66X501 3.3 43.2 1.0 HG13 A:VAL78 3.3 25.4 1.0 C31 A:66X501 3.4 25.2 1.0 HG11 A:VAL78 3.5 25.4 1.0 HD21 A:LEU70 3.5 54.4 1.0 HD21 A:LEU142 3.6 22.9 1.0 H29 A:66X501 3.6 30.2 1.0 HD13 A:LEU73 3.6 35.3 1.0 HD11 A:LEU142 3.7 35.3 1.0 CG1 A:VAL78 3.8 21.1 1.0 HG12 A:VAL78 3.9 25.4 1.0 HD23 A:LEU70 3.9 54.4 1.0 H27 A:66X501 4.0 61.8 1.0 H28 A:66X501 4.1 61.8 1.0 HD22 A:LEU142 4.2 22.9 1.0 HD13 A:LEU142 4.2 35.3 1.0 N24 A:66X501 4.2 44.9 1.0 CD2 A:LEU70 4.2 45.3 1.0 C21 A:66X501 4.3 29.1 1.0 HG22 A:ILE79 4.3 42.8 1.0 C29 A:66X501 4.3 51.5 1.0 CD2 A:LEU142 4.3 19.1 1.0 CD1 A:LEU142 4.4 29.4 1.0 CD1 A:LEU73 4.4 29.4 1.0 HD12 A:LEU73 4.5 35.3 1.0 HG22 A:ILE171 4.5 27.6 1.0 C19 A:66X501 4.6 25.3 1.0 HD11 A:LEU73 4.7 35.3 1.0 HA A:ALA172 4.7 35.4 1.0 H22 A:66X501 4.7 61.3 1.0 HD2 A:HIS149 4.8 34.0 1.0 HG A:LEU70 4.8 52.3 1.0 HD22 A:LEU70 4.9 54.4 1.0 C20 A:66X501 4.9 37.8 1.0 HG11 A:VAL147 5.0 34.6 1.0 H17 A:66X501 5.0 34.9 1.0

P.Bergeron, M.F.Koehler, E.M.Blackwood, K.Bowman, K.Clark, R.Firestein, J.R.Kiefer, K.Maskos, M.L.Mccleland, L.Orren, S.Ramaswamy, L.Salphati, S.Schmidt, E.V.Schneider, J.Wu, M.Beresini. Design and Development of A Series of Potent and Selective Type II Inhibitors of CDK8. Acs Med.Chem.Lett. V. 7 595 2016.
ISSN: ISSN 1948-5875
PubMed: 27326333
DOI: 10.1021/ACSMEDCHEMLETT.6B00044