Fluorine in PDB 5iev: Crystal Structure of Bay 1000394 (Roniciclib) Bound to CDK2

All present enzymatic activity of Crystal Structure of Bay 1000394 (Roniciclib) Bound to CDK2:
2.7.11.22;

The structure of Crystal Structure of Bay 1000394 (Roniciclib) Bound to CDK2, PDB code: 5iev was solved by P.Ayaz, D.Andres, D.A.Kwiatkowski, C.Kolbe, P.Lienau, G.Siemeister, U.Luecking, C.M.Stegmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.28 / 2.03
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.776, 71.814, 72.901, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 26.2

The binding sites of Fluorine atom in the Crystal Structure of Bay 1000394 (Roniciclib) Bound to CDK2 (pdb code 5iev). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Bay 1000394 (Roniciclib) Bound to CDK2, PDB code: 5iev:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Bay 1000394 (Roniciclib) Bound to CDK2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Bay 1000394 (Roniciclib) Bound to CDK2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:12.6 occ:1.00 F3 A:R0N1001 0.0 12.6 1.0 C2 A:R0N1001 1.4 13.2 1.0 F4 A:R0N1001 2.2 12.2 1.0 F1 A:R0N1001 2.3 13.4 1.0 C5 A:R0N1001 2.4 12.8 1.0 C10 A:R0N1001 2.6 13.3 1.0 CB A:PHE80 2.8 10.8 1.0 CG A:PHE80 3.2 11.0 1.0 CG2 A:VAL64 3.4 12.8 1.0 CD2 A:PHE80 3.6 11.8 1.0 O A:GLU81 3.6 10.1 1.0 C6 A:R0N1001 3.7 14.5 1.0 CB A:ALA31 3.7 11.5 1.0 CD1 A:PHE80 3.8 11.2 1.0 O A:HOH1196 3.9 50.7 1.0 N9 A:R0N1001 4.0 13.4 1.0 O24 A:R0N1001 4.3 14.1 1.0 CA A:PHE80 4.3 10.7 1.0 CG1 A:VAL64 4.3 14.6 1.0 CB A:VAL64 4.4 13.1 1.0 CE2 A:PHE80 4.5 12.0 1.0 CD1 A:LEU134 4.6 12.2 1.0 C A:PHE80 4.7 9.9 1.0 N7 A:R0N1001 4.7 15.0 1.0 CE1 A:PHE80 4.7 11.6 1.0 C A:GLU81 4.8 9.9 1.0 C8 A:R0N1001 4.8 14.3 1.0 N A:GLU81 4.9 9.6 1.0 O A:HOH1190 5.0 40.2 1.0 CB A:ALA144 5.0 15.1 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Bay 1000394 (Roniciclib) Bound to CDK2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Bay 1000394 (Roniciclib) Bound to CDK2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:12.2 occ:1.00 F4 A:R0N1001 0.0 12.2 1.0 C2 A:R0N1001 1.3 13.2 1.0 F1 A:R0N1001 2.1 13.4 1.0 F3 A:R0N1001 2.2 12.6 1.0 C5 A:R0N1001 2.3 12.8 1.0 C6 A:R0N1001 3.0 14.5 1.0 O24 A:R0N1001 3.1 14.1 1.0 C10 A:R0N1001 3.3 13.3 1.0 CB A:ALA31 3.5 11.5 1.0 CG1 A:VAL18 3.5 21.0 1.0 O A:HOH1190 3.6 40.2 1.0 CD2 A:PHE80 3.7 11.8 1.0 O A:HOH1196 3.9 50.7 1.0 CB A:PHE80 4.1 10.8 1.0 CG A:PHE80 4.1 11.0 1.0 N7 A:R0N1001 4.2 15.0 1.0 C25 A:R0N1001 4.4 13.6 1.0 CG2 A:VAL18 4.4 19.6 1.0 N9 A:R0N1001 4.4 13.4 1.0 CE2 A:PHE80 4.5 12.0 1.0 O27 A:R0N1001 4.6 15.6 1.0 CB A:VAL18 4.6 19.4 1.0 CA A:ALA31 4.7 11.8 1.0 C A:ALA31 4.8 13.2 1.0 O A:ALA31 4.8 13.7 1.0 C8 A:R0N1001 4.8 14.3 1.0 C26 A:R0N1001 4.9 14.4 1.0 C28 A:R0N1001 5.0 14.8 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Bay 1000394 (Roniciclib) Bound to CDK2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Bay 1000394 (Roniciclib) Bound to CDK2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:13.4 occ:1.00 F1 A:R0N1001 0.0 13.4 1.0 C2 A:R0N1001 1.4 13.2 1.0 F4 A:R0N1001 2.1 12.2 1.0 F3 A:R0N1001 2.3 12.6 1.0 C5 A:R0N1001 2.4 12.8 1.0 O A:HOH1196 2.8 50.7 1.0 O24 A:R0N1001 2.9 14.1 1.0 C6 A:R0N1001 2.9 14.5 1.0 O A:HOH1190 3.2 40.2 1.0 CB A:ALA144 3.5 15.1 1.0 C10 A:R0N1001 3.5 13.3 1.0 C28 A:R0N1001 3.5 14.8 1.0 C25 A:R0N1001 4.0 13.6 1.0 CD1 A:LEU134 4.1 12.2 1.0 C26 A:R0N1001 4.1 14.4 1.0 O27 A:R0N1001 4.1 15.6 1.0 N7 A:R0N1001 4.2 15.0 1.0 CG1 A:VAL64 4.5 14.6 1.0 CD2 A:PHE80 4.5 11.8 1.0 CG2 A:VAL64 4.6 12.8 1.0 CG A:PHE80 4.6 11.0 1.0 CA A:ALA144 4.6 15.7 1.0 N9 A:R0N1001 4.6 13.4 1.0 N A:ASP145 4.6 22.6 1.0 CB A:ASP145 4.9 31.3 1.0 CB A:PHE80 4.9 10.8 1.0 C8 A:R0N1001 4.9 14.3 1.0 CE2 A:PHE80 4.9 12.0 1.0 C A:ALA144 5.0 17.3 1.0 CB A:VAL64 5.0 13.1 1.0

P.Ayaz, D.Andres, D.A.Kwiatkowski, C.C.Kolbe, P.Lienau, G.Siemeister, U.Lucking, C.M.Stegmann. Conformational Adaption May Explain the Slow Dissociation Kinetics of Roniciclib (Bay 1000394), A Type I Cdk Inhibitor with Kinetic Selectivity For CDK2 and CDK9. Acs Chem.Biol. V. 11 1710 2016.
ISSN: ESSN 1554-8937
PubMed: 27090615
DOI: 10.1021/ACSCHEMBIO.6B00074