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Fluorine in PDB 5n33: Camp-Dependent Protein Kinase A From Cricetulus Griseus in Complex with Fragment Like Molecule 3-Amino-5-(Trifluoromethyl)-1H-Pyridin-2- One

Enzymatic activity of Camp-Dependent Protein Kinase A From Cricetulus Griseus in Complex with Fragment Like Molecule 3-Amino-5-(Trifluoromethyl)-1H-Pyridin-2- One

All present enzymatic activity of Camp-Dependent Protein Kinase A From Cricetulus Griseus in Complex with Fragment Like Molecule 3-Amino-5-(Trifluoromethyl)-1H-Pyridin-2- One:
2.7.11.11;

Protein crystallography data

The structure of Camp-Dependent Protein Kinase A From Cricetulus Griseus in Complex with Fragment Like Molecule 3-Amino-5-(Trifluoromethyl)-1H-Pyridin-2- One, PDB code: 5n33 was solved by 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) 41.91 / 1.43
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.225, 72.589, 108.793, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 17.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Camp-Dependent Protein Kinase A From Cricetulus Griseus in Complex with Fragment Like Molecule 3-Amino-5-(Trifluoromethyl)-1H-Pyridin-2- One (pdb code 5n33). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Camp-Dependent Protein Kinase A From Cricetulus Griseus in Complex with Fragment Like Molecule 3-Amino-5-(Trifluoromethyl)-1H-Pyridin-2- One, PDB code: 5n33:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5n33

Go back to Fluorine Binding Sites List in 5n33
Fluorine binding site 1 out of 3 in the Camp-Dependent Protein Kinase A From Cricetulus Griseus in Complex with Fragment Like Molecule 3-Amino-5-(Trifluoromethyl)-1H-Pyridin-2- One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Camp-Dependent Protein Kinase A From Cricetulus Griseus in Complex with Fragment Like Molecule 3-Amino-5-(Trifluoromethyl)-1H-Pyridin-2- One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:22.2
occ:1.00
 F2 A:8JW401 0.0 22.2 1.0
C5 A:8JW401 1.3 22.1 1.0
F A:8JW401 2.1 23.1 1.0
F1 A:8JW401 2.2 24.0 1.0
C1 A:8JW401 2.3 19.2 1.0
H2 A:8JW401 2.5 22.1 1.0
HG3 A:MET120 2.7 27.9 0.4
HB A:THR183 2.7 24.4 1.0
C2 A:8JW401 2.7 18.4 1.0
HE1 A:MET120 3.0 31.4 0.6
HE3 A:MET120 3.1 31.4 0.6
O A:HOH544 3.1 30.1 1.0
SD A:MET120 3.2 26.5 0.6
CE A:MET120 3.2 26.2 0.6
HG11 A:VAL104 3.3 26.0 1.0
H A:ASP184 3.5 26.2 1.0
HE2 A:MET120 3.6 28.3 0.4
CB A:THR183 3.6 20.3 1.0
HG22 A:THR183 3.6 26.5 1.0
C A:8JW401 3.6 18.9 1.0
CG A:MET120 3.6 23.3 0.4
HG21 A:VAL104 3.7 24.3 1.0
HG21 A:THR183 3.8 26.5 1.0
HB2 A:MET120 3.8 27.2 0.6
CG2 A:THR183 3.8 22.1 1.0
H1 A:8JW401 3.9 22.7 1.0
O A:HOH700 4.0 51.8 1.0
HB3 A:MET120 4.0 25.8 0.4
HB2 A:MET120 4.1 25.8 0.4
N A:8JW401 4.1 18.1 1.0
HA A:THR183 4.1 23.9 1.0
HG2 A:MET120 4.1 27.9 0.4
CB A:MET120 4.2 21.5 0.4
HE2 A:MET120 4.2 31.4 0.6
CG1 A:VAL104 4.2 21.6 1.0
N A:ASP184 4.3 21.9 1.0
HB3 A:MET120 4.3 27.2 0.6
CE A:MET120 4.4 23.6 0.4
CA A:THR183 4.4 19.9 1.0
CB A:MET120 4.4 22.7 0.6
CG A:MET120 4.5 24.9 0.6
HG13 A:VAL104 4.5 26.0 1.0
OG1 A:THR183 4.5 19.9 1.0
SD A:MET120 4.6 24.5 0.4
CG2 A:VAL104 4.6 20.3 1.0
HE3 A:MET120 4.6 28.3 0.4
H A:8JW401 4.6 21.7 1.0
HD2 A:LYS72 4.7 30.8 1.0
C4 A:8JW401 4.7 18.3 1.0
HB2 A:LYS72 4.8 28.2 1.0
HG12 A:VAL104 4.8 26.0 1.0
HG23 A:THR183 4.8 26.5 1.0
HG22 A:VAL104 4.9 24.3 1.0
HG21 A:VAL57 4.9 26.0 1.0
HB3 A:ALA70 4.9 24.8 1.0
C A:THR183 4.9 19.9 1.0
CB A:VAL104 4.9 19.8 1.0
HA A:ASP184 4.9 25.6 1.0
HB A:VAL104 5.0 23.7 1.0
C3 A:8JW401 5.0 19.0 1.0
HG11 A:VAL57 5.0 25.6 1.0

Fluorine binding site 2 out of 3 in 5n33

Go back to Fluorine Binding Sites List in 5n33
Fluorine binding site 2 out of 3 in the Camp-Dependent Protein Kinase A From Cricetulus Griseus in Complex with Fragment Like Molecule 3-Amino-5-(Trifluoromethyl)-1H-Pyridin-2- One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Camp-Dependent Protein Kinase A From Cricetulus Griseus in Complex with Fragment Like Molecule 3-Amino-5-(Trifluoromethyl)-1H-Pyridin-2- One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:23.1
occ:1.00
 F A:8JW401 0.0 23.1 1.0
C5 A:8JW401 1.3 22.1 1.0
F1 A:8JW401 2.1 24.0 1.0
F2 A:8JW401 2.1 22.2 1.0
C1 A:8JW401 2.3 19.2 1.0
HB A:THR183 2.5 24.4 1.0
H1 A:8JW401 2.6 22.7 1.0
C A:8JW401 2.8 18.9 1.0
O A:HOH700 3.1 51.8 1.0
O A:HOH778 3.2 47.5 1.0
CB A:THR183 3.3 20.3 1.0
C2 A:8JW401 3.5 18.4 1.0
HG21 A:THR183 3.5 26.5 1.0
OG1 A:THR183 3.6 19.9 1.0
HG21 A:VAL57 3.6 26.0 1.0
H A:ASP184 3.7 26.2 1.0
O A:HOH601 3.7 31.7 1.0
H2 A:8JW401 3.8 22.1 1.0
CG2 A:THR183 3.9 22.1 1.0
O A:HOH544 4.1 30.1 1.0
C4 A:8JW401 4.1 18.3 1.0
HG22 A:THR183 4.1 26.5 1.0
N A:ASP184 4.2 21.9 1.0
HE1 A:MET120 4.2 31.4 0.6
HG11 A:VAL57 4.2 25.6 1.0
HB2 A:ASP184 4.3 28.8 1.0
HG1 A:THR183 4.4 23.9 1.0
CG2 A:VAL57 4.5 21.6 1.0
HD11 A:LEU173 4.5 29.0 1.0
CA A:THR183 4.5 19.9 1.0
HG3 A:MET120 4.5 27.9 0.4
HG22 A:VAL57 4.5 26.0 1.0
HD2 A:LYS72 4.6 30.8 1.0
HE3 A:MET120 4.6 31.4 0.6
N A:8JW401 4.6 18.1 1.0
HA A:THR183 4.7 23.9 1.0
HA A:ASP184 4.7 25.6 1.0
C A:THR183 4.7 19.9 1.0
CE A:MET120 4.8 26.2 0.6
HG23 A:THR183 4.8 26.5 1.0
CA A:ASP184 4.9 21.3 1.0
HG11 A:VAL104 4.9 26.0 1.0
O A:HOH626 4.9 16.9 0.5
C3 A:8JW401 4.9 19.0 1.0
O A:HOH787 4.9 38.5 1.0

Fluorine binding site 3 out of 3 in 5n33

Go back to Fluorine Binding Sites List in 5n33
Fluorine binding site 3 out of 3 in the Camp-Dependent Protein Kinase A From Cricetulus Griseus in Complex with Fragment Like Molecule 3-Amino-5-(Trifluoromethyl)-1H-Pyridin-2- One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Camp-Dependent Protein Kinase A From Cricetulus Griseus in Complex with Fragment Like Molecule 3-Amino-5-(Trifluoromethyl)-1H-Pyridin-2- One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:24.0
occ:1.00
 F1 A:8JW401 0.0 24.0 1.0
C5 A:8JW401 1.3 22.1 1.0
F A:8JW401 2.1 23.1 1.0
F2 A:8JW401 2.2 22.2 1.0
C1 A:8JW401 2.3 19.2 1.0
HE1 A:MET120 2.7 31.4 0.6
HE3 A:MET120 2.8 31.4 0.6
HG21 A:VAL57 2.9 26.0 1.0
H1 A:8JW401 3.0 22.7 1.0
C A:8JW401 3.0 18.9 1.0
HG11 A:VAL57 3.2 25.6 1.0
HG3 A:MET120 3.2 27.9 0.4
CE A:MET120 3.2 26.2 0.6
HG22 A:VAL57 3.2 26.0 1.0
HB2 A:LYS72 3.2 28.2 1.0
C2 A:8JW401 3.3 18.4 1.0
HG13 A:VAL57 3.5 25.6 1.0
CG2 A:VAL57 3.5 21.6 1.0
H2 A:8JW401 3.6 22.1 1.0
O A:HOH700 3.7 51.8 1.0
HD2 A:LYS72 3.7 30.8 1.0
CG1 A:VAL57 3.7 21.3 1.0
HE2 A:MET120 4.0 31.4 0.6
CG A:MET120 4.0 23.3 0.4
HG2 A:MET120 4.0 27.9 0.4
HB1 A:ALA70 4.1 24.8 1.0
HB A:THR183 4.2 24.4 1.0
SD A:MET120 4.2 26.5 0.6
CB A:LYS72 4.2 23.5 1.0
O A:HOH544 4.2 30.1 1.0
CB A:VAL57 4.3 20.4 1.0
C4 A:8JW401 4.3 18.3 1.0
HG23 A:VAL57 4.3 26.0 1.0
HB2 A:MET120 4.3 27.2 0.6
HB3 A:ALA70 4.4 24.8 1.0
O A:HOH778 4.5 47.5 1.0
N A:8JW401 4.5 18.1 1.0
HB2 A:MET120 4.5 25.8 0.4
CD A:LYS72 4.6 25.7 1.0
HG12 A:VAL57 4.6 25.6 1.0
HB3 A:LYS72 4.7 28.2 1.0
HG3 A:LYS72 4.7 29.4 1.0
CB A:ALA70 4.7 20.6 1.0
HB A:VAL57 4.8 24.4 1.0
CG A:LYS72 4.8 24.5 1.0
CB A:MET120 4.8 21.5 0.4
H A:LYS72 4.8 25.0 0.4
H A:LYS72 4.8 25.0 0.6
HA A:LYS72 4.8 24.8 1.0
H A:ASP184 4.9 26.2 1.0
N A:LYS72 4.9 20.8 1.0
C3 A:8JW401 4.9 19.0 1.0
HD3 A:LYS72 4.9 30.8 1.0
CA A:LYS72 4.9 20.7 1.0
O A:ALA70 5.0 22.8 1.0

Reference:

C.Siefker, A.Heine, G.Klebe. A Crystallographic Fragment Study with Camp-Dependent Protein Kinase A To Be Published.
Page generated: Tue Jul 15 05:25:15 2025

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