Fluorine in PDB 6sps: Crystal Structure of Camp-Dependent Protein Kinase A (Cho Pka) in Complex with 4-(Trifluoromethyl)Benzamide

All present enzymatic activity of Crystal Structure of Camp-Dependent Protein Kinase A (Cho Pka) in Complex with 4-(Trifluoromethyl)Benzamide:
2.7.11.11;

The structure of Crystal Structure of Camp-Dependent Protein Kinase A (Cho Pka) in Complex with 4-(Trifluoromethyl)Benzamide, PDB code: 6sps was solved by M.Oebbeke, C.Siefker, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.65 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.669, 71.282, 97.448, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.3

The binding sites of Fluorine atom in the Crystal Structure of Camp-Dependent Protein Kinase A (Cho Pka) in Complex with 4-(Trifluoromethyl)Benzamide (pdb code 6sps). 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 Camp-Dependent Protein Kinase A (Cho Pka) in Complex with 4-(Trifluoromethyl)Benzamide, PDB code: 6sps:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Camp-Dependent Protein Kinase A (Cho Pka) in Complex with 4-(Trifluoromethyl)Benzamide


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 Camp-Dependent Protein Kinase A (Cho Pka) in Complex with 4-(Trifluoromethyl)Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:30.8 occ:1.00 F A:LR5403 0.0 30.8 1.0 C5 A:LR5403 1.3 24.2 1.0 F2 A:LR5403 2.1 25.4 1.0 F1 A:LR5403 2.1 29.8 1.0 C4 A:LR5403 2.3 14.8 1.0 C3 A:LR5403 2.7 14.9 1.0 C6 A:LR5403 3.6 15.9 1.0 C2 A:LR5403 4.1 14.6 1.0 CG2 A:VAL57 4.1 18.9 1.0 OE2 A:GLU127 4.1 27.6 1.0 CB A:VAL57 4.4 15.4 1.0 CA A:GLY50 4.7 23.0 1.0 C7 A:LR5403 4.8 13.9 1.0 CG1 A:VAL57 4.9 16.6 1.0 C1 A:LR5403 5.0 12.9 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Camp-Dependent Protein Kinase A (Cho Pka) in Complex with 4-(Trifluoromethyl)Benzamide


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 Camp-Dependent Protein Kinase A (Cho Pka) in Complex with 4-(Trifluoromethyl)Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:29.8 occ:1.00 F1 A:LR5403 0.0 29.8 1.0 C5 A:LR5403 1.3 24.2 1.0 F2 A:LR5403 2.1 25.4 1.0 F A:LR5403 2.1 30.8 1.0 C4 A:LR5403 2.3 14.8 1.0 C6 A:LR5403 2.9 15.9 1.0 OE2 A:GLU127 2.9 27.6 1.0 C3 A:LR5403 3.5 14.9 1.0 O A:LEU49 3.7 19.5 1.0 CD A:GLU127 4.0 27.2 1.0 CE1 A:PHE327 4.1 18.5 1.0 CD1 A:PHE327 4.2 19.7 1.0 C7 A:LR5403 4.2 13.9 1.0 C A:LEU49 4.4 16.2 1.0 CG A:GLU127 4.5 21.5 1.0 CA A:GLY50 4.5 23.0 1.0 C2 A:LR5403 4.6 14.6 1.0 O A:HOH593 4.7 32.6 1.0 N A:GLY50 4.7 17.7 1.0 CB A:LEU49 4.7 17.2 1.0 C1 A:LR5403 4.9 12.9 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Camp-Dependent Protein Kinase A (Cho Pka) in Complex with 4-(Trifluoromethyl)Benzamide


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 Camp-Dependent Protein Kinase A (Cho Pka) in Complex with 4-(Trifluoromethyl)Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:25.4 occ:1.00 F2 A:LR5403 0.0 25.4 1.0 C5 A:LR5403 1.3 24.2 1.0 F1 A:LR5403 2.1 29.8 1.0 F A:LR5403 2.1 30.8 1.0 C4 A:LR5403 2.3 14.8 1.0 C6 A:LR5403 3.0 15.9 1.0 N A:GLY50 3.3 17.7 1.0 CA A:GLY50 3.3 23.0 1.0 C A:LEU49 3.3 16.2 1.0 O A:LEU49 3.3 19.5 1.0 C3 A:LR5403 3.4 14.9 1.0 CB A:VAL57 3.4 15.4 1.0 CB A:LEU49 3.7 17.2 1.0 CG1 A:VAL57 4.0 16.6 1.0 CG2 A:VAL57 4.0 18.9 1.0 CA A:LEU49 4.1 17.6 1.0 C A:GLY50 4.3 23.0 1.0 C7 A:LR5403 4.3 13.9 1.0 O A:VAL57 4.5 17.0 1.0 O A:GLY50 4.5 20.6 1.0 C2 A:LR5403 4.6 14.6 1.0 CA A:VAL57 4.6 13.2 1.0 N A:VAL57 4.8 14.8 1.0 C A:VAL57 4.9 14.7 1.0 OE2 A:GLU127 5.0 27.6 1.0 C1 A:LR5403 5.0 12.9 1.0 N A:LEU49 5.0 16.4 1.0

M.Oebbeke, C.Siefker, B.Wagner, A.Heine, G.Klebe. Fragment Binding to Kinase Hinge: if Charge Distribution and Local Pk A Shifts Mislead Popular Bioisosterism Concepts. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 33021032
DOI: 10.1002/ANIE.202011295