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: Thu Aug 1 11:55:04 2024
|