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

Enzymatic activity of Crystal Structure of Camp-Dependent Protein Kinase A (Cho Pka) in Complex with 4-(Trifluoromethyl)Benzoic Acid

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

Protein crystallography data

The structure of Crystal Structure of Camp-Dependent Protein Kinase A (Cho Pka) in Complex with 4-(Trifluoromethyl)Benzoic Acid, PDB code: 6spm 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) 38.44 / 1.37
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.556, 71.403, 97.810, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 17

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 3 in 6spm

Go back to Fluorine Binding Sites List in 6spm
Fluorine binding site 1 out of 3 in the Crystal Structure of Camp-Dependent Protein Kinase A (Cho Pka) in Complex with 4-(Trifluoromethyl)Benzoic Acid


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)Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:21.4
occ:1.00
 F01 A:3AE401 0.0 21.4 1.0
C07 A:3AE401 1.3 21.9 1.0
F02 A:3AE401 2.1 23.4 1.0
F A:3AE401 2.1 24.8 1.0
C05 A:3AE401 2.3 17.8 1.0
HB A:VAL57 2.5 15.8 1.0
HA3 A:GLY50 2.7 22.4 1.0
C A:3AE401 3.0 16.0 1.0
HG21 A:VAL57 3.3 17.2 1.0
HB2 A:LEU49 3.3 17.6 1.0
CB A:VAL57 3.4 13.2 1.0
C04 A:3AE401 3.4 16.1 1.0
CA A:GLY50 3.5 18.7 1.0
O A:LEU49 3.5 18.2 1.0
N A:GLY50 3.5 17.2 1.0
C A:LEU49 3.6 16.6 1.0
HG11 A:VAL57 3.6 15.9 1.0
CG2 A:VAL57 3.7 14.4 1.0
HB3 A:LEU49 3.7 17.6 1.0
HG23 A:VAL57 3.8 17.2 1.0
CG1 A:VAL57 3.9 13.3 1.0
CB A:LEU49 3.9 14.7 1.0
HG12 A:VAL57 3.9 15.9 1.0
H A:GLY50 4.0 20.7 1.0
HA2 A:GLY50 4.1 22.4 1.0
C01 A:3AE401 4.3 14.1 1.0
CA A:LEU49 4.4 14.6 1.0
H A:VAL57 4.4 15.3 0.6
C A:GLY50 4.5 19.7 1.0
H A:VAL57 4.5 15.3 0.5
CA A:VAL57 4.6 12.1 1.0
C06 A:3AE401 4.6 14.8 1.0
HG22 A:VAL57 4.6 17.2 1.0
O A:GLY50 4.7 18.0 1.0
O A:HOH664 4.7 19.0 0.5
O A:VAL57 4.7 11.9 1.0
N A:VAL57 4.8 12.7 1.0
HG13 A:VAL57 4.8 15.9 1.0
C02 A:3AE401 4.9 13.4 1.0
HD1 A:PHE327 5.0 16.9 1.0
HD12 A:LEU49 5.0 19.2 1.0

Fluorine binding site 2 out of 3 in 6spm

Go back to Fluorine Binding Sites List in 6spm
Fluorine binding site 2 out of 3 in the Crystal Structure of Camp-Dependent Protein Kinase A (Cho Pka) in Complex with 4-(Trifluoromethyl)Benzoic Acid


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)Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:23.4
occ:1.00
 F02 A:3AE401 0.0 23.4 1.0
C07 A:3AE401 1.3 21.9 1.0
F01 A:3AE401 2.1 21.4 1.0
F A:3AE401 2.1 24.8 1.0
C05 A:3AE401 2.3 17.8 1.0
O A:HOH664 2.9 19.0 0.5
C A:3AE401 2.9 16.0 1.0
OE2 A:GLU127 3.1 21.6 1.0
C04 A:3AE401 3.4 16.1 1.0
O A:HOH664 3.7 20.1 0.5
HE1 A:PHE327 3.8 17.4 1.0
HA3 A:GLY50 4.0 22.4 1.0
HD1 A:PHE327 4.1 16.9 1.0
O A:LEU49 4.2 18.2 1.0
C01 A:3AE401 4.2 14.1 1.0
CD A:GLU127 4.3 19.3 1.0
CE1 A:PHE327 4.4 14.5 1.0
HG3 A:GLU127 4.5 18.0 1.0
HG2 A:GLU127 4.5 18.0 1.0
HD21 A:LEU173 4.5 16.9 1.0
HB A:VAL57 4.5 15.8 1.0
HB3 A:LEU49 4.6 17.6 1.0
C06 A:3AE401 4.6 14.8 1.0
CD1 A:PHE327 4.6 14.1 1.0
HG21 A:VAL57 4.7 17.2 1.0
CG A:GLU127 4.7 15.0 1.0
C A:LEU49 4.8 16.6 1.0
CA A:GLY50 4.8 18.7 1.0
HB2 A:LEU49 4.8 17.6 1.0
C02 A:3AE401 4.9 13.4 1.0
HG21 A:THR183 5.0 16.5 1.0

Fluorine binding site 3 out of 3 in 6spm

Go back to Fluorine Binding Sites List in 6spm
Fluorine binding site 3 out of 3 in the Crystal Structure of Camp-Dependent Protein Kinase A (Cho Pka) in Complex with 4-(Trifluoromethyl)Benzoic Acid


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)Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:24.8
occ:1.00
 F A:3AE401 0.0 24.8 1.0
C07 A:3AE401 1.3 21.9 1.0
F01 A:3AE401 2.1 21.4 1.0
F02 A:3AE401 2.1 23.4 1.0
C05 A:3AE401 2.4 17.8 1.0
C04 A:3AE401 2.7 16.1 1.0
HG21 A:VAL57 3.0 17.2 1.0
O A:HOH664 3.3 20.1 0.5
O A:HOH664 3.3 19.0 0.5
C A:3AE401 3.6 16.0 1.0
HB A:VAL57 3.7 15.8 1.0
HG23 A:VAL57 3.7 17.2 1.0
CG2 A:VAL57 3.7 14.4 1.0
HA3 A:GLY50 4.1 22.4 1.0
C06 A:3AE401 4.1 14.8 1.0
CB A:VAL57 4.2 13.2 1.0
HG11 A:VAL57 4.2 15.9 1.0
HG22 A:VAL57 4.5 17.2 1.0
HG21 A:THR183 4.6 16.5 1.0
CG1 A:VAL57 4.8 13.3 1.0
OE2 A:GLU127 4.8 21.6 1.0
C01 A:3AE401 4.8 14.1 1.0
HG23 A:THR183 4.9 16.5 1.0
C02 A:3AE401 5.0 13.4 1.0
CA A:GLY50 5.0 18.7 1.0

Reference:

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
Page generated: Tue Jul 15 15:44:45 2025

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