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Fluorine in PDB 5n3d: Camp-Dependent Protein Kinase A From Cricetulus Griseus in Complex with Fragment Like Molecule 4-(Trifluoromethyl)Benzenecarboximidamide

Enzymatic activity of Camp-Dependent Protein Kinase A From Cricetulus Griseus in Complex with Fragment Like Molecule 4-(Trifluoromethyl)Benzenecarboximidamide

All present enzymatic activity of Camp-Dependent Protein Kinase A From Cricetulus Griseus in Complex with Fragment Like Molecule 4-(Trifluoromethyl)Benzenecarboximidamide:
2.7.11.11;

Protein crystallography data

The structure of Camp-Dependent Protein Kinase A From Cricetulus Griseus in Complex with Fragment Like Molecule 4-(Trifluoromethyl)Benzenecarboximidamide, PDB code: 5n3d 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) 45.46 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.419, 72.389, 108.383, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 19.3

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 4-(Trifluoromethyl)Benzenecarboximidamide (pdb code 5n3d). 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 4-(Trifluoromethyl)Benzenecarboximidamide, PDB code: 5n3d:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5n3d

Go back to Fluorine Binding Sites List in 5n3d
Fluorine binding site 1 out of 3 in the Camp-Dependent Protein Kinase A From Cricetulus Griseus in Complex with Fragment Like Molecule 4-(Trifluoromethyl)Benzenecarboximidamide


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 4-(Trifluoromethyl)Benzenecarboximidamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:48.9
occ:0.88
 F11 A:8NE401 0.0 48.9 0.9
C10 A:8NE401 1.3 48.5 0.9
F12 A:8NE401 2.1 49.2 0.9
F13 A:8NE401 2.1 50.5 0.9
C3 A:8NE401 2.3 44.9 0.9
H4 A:8NE401 2.6 50.9 0.9
C4 A:8NE401 2.8 42.4 0.9
HG21 A:VAL57 2.9 34.6 1.0
HA3 A:GLY50 3.4 31.4 1.0
C2 A:8NE401 3.6 42.4 0.9
HB A:VAL57 3.6 31.7 1.0
HG23 A:VAL57 3.6 34.6 1.0
CG2 A:VAL57 3.6 28.8 1.0
H2 A:8NE401 3.9 50.9 0.9
O A:HOH632 4.1 42.9 1.0
CB A:VAL57 4.1 26.4 1.0
HG11 A:VAL57 4.1 33.2 1.0
C5 A:8NE401 4.2 40.6 0.9
O A:HOH611 4.3 33.8 1.0
OE2 A:GLU127 4.4 24.1 1.0
CA A:GLY50 4.4 26.2 1.0
HG22 A:VAL57 4.5 34.6 1.0
CG1 A:VAL57 4.7 27.7 1.0
C1 A:8NE401 4.7 40.6 0.9
H5 A:8NE401 4.9 48.7 0.9
N A:GLY50 4.9 24.4 1.0
C A:GLY50 4.9 28.4 1.0
O A:LEU49 4.9 26.0 1.0
HA2 A:GLY50 5.0 31.4 1.0

Fluorine binding site 2 out of 3 in 5n3d

Go back to Fluorine Binding Sites List in 5n3d
Fluorine binding site 2 out of 3 in the Camp-Dependent Protein Kinase A From Cricetulus Griseus in Complex with Fragment Like Molecule 4-(Trifluoromethyl)Benzenecarboximidamide


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 4-(Trifluoromethyl)Benzenecarboximidamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:49.2
occ:0.88
 F12 A:8NE401 0.0 49.2 0.9
C10 A:8NE401 1.3 48.5 0.9
F11 A:8NE401 2.1 48.9 0.9
F13 A:8NE401 2.1 50.5 0.9
C3 A:8NE401 2.3 44.9 0.9
H2 A:8NE401 2.5 50.9 0.9
HA3 A:GLY50 2.7 31.4 1.0
C2 A:8NE401 2.7 42.4 0.9
O A:LEU49 3.0 26.0 1.0
OE2 A:GLU127 3.4 24.1 1.0
O A:HOH525 3.4 29.0 1.0
CA A:GLY50 3.5 26.2 1.0
C A:LEU49 3.5 24.2 1.0
C4 A:8NE401 3.6 42.4 0.9
N A:GLY50 3.7 24.4 1.0
HB A:VAL57 3.7 31.7 1.0
HB3 A:LEU49 3.8 27.1 1.0
HA2 A:GLY50 3.9 31.4 1.0
H4 A:8NE401 4.0 50.9 0.9
HB2 A:LEU49 4.0 27.1 1.0
C1 A:8NE401 4.1 40.6 0.9
HE1 A:PHE327 4.1 27.9 1.0
O A:HOH632 4.2 42.9 1.0
HD1 A:PHE327 4.3 29.1 1.0
CB A:LEU49 4.3 22.6 1.0
HG21 A:VAL57 4.3 34.6 1.0
H A:GLY50 4.3 29.3 1.0
CD A:GLU127 4.5 24.3 1.0
HG11 A:VAL57 4.5 33.2 1.0
CA A:LEU49 4.6 22.7 1.0
CB A:VAL57 4.6 26.4 1.0
HG3 A:GLU127 4.6 21.6 1.0
C A:GLY50 4.6 28.4 1.0
CE1 A:PHE327 4.7 23.2 1.0
C5 A:8NE401 4.7 40.6 0.9
HD21 A:LEU173 4.7 37.2 1.0
H1 A:8NE401 4.8 48.7 0.9
HG2 A:GLU127 4.8 21.6 1.0
CD1 A:PHE327 4.8 24.2 1.0
CG2 A:VAL57 4.8 28.8 1.0
HG23 A:VAL57 4.9 34.6 1.0
CG A:GLU127 4.9 18.0 1.0
O A:HOH629 4.9 26.1 1.0
C6 A:8NE401 5.0 36.9 0.9
CG1 A:VAL57 5.0 27.7 1.0

Fluorine binding site 3 out of 3 in 5n3d

Go back to Fluorine Binding Sites List in 5n3d
Fluorine binding site 3 out of 3 in the Camp-Dependent Protein Kinase A From Cricetulus Griseus in Complex with Fragment Like Molecule 4-(Trifluoromethyl)Benzenecarboximidamide


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 4-(Trifluoromethyl)Benzenecarboximidamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:50.5
occ:0.88
 F13 A:8NE401 0.0 50.5 0.9
C10 A:8NE401 1.3 48.5 0.9
F12 A:8NE401 2.1 49.2 0.9
F11 A:8NE401 2.1 48.9 0.9
C3 A:8NE401 2.4 44.9 0.9
OE2 A:GLU127 2.8 24.1 1.0
C4 A:8NE401 3.2 42.4 0.9
C2 A:8NE401 3.2 42.4 0.9
H4 A:8NE401 3.3 50.9 0.9
HG2 A:GLU127 3.4 21.6 1.0
HD21 A:LEU173 3.4 37.2 1.0
H2 A:8NE401 3.4 50.9 0.9
CD A:GLU127 3.7 24.3 1.0
O A:HOH632 3.8 42.9 1.0
CG A:GLU127 3.8 18.0 1.0
O A:GLU170 3.9 17.2 1.0
HG3 A:GLU127 3.9 21.6 1.0
HG1 A:THR183 4.2 51.1 1.0
HE1 A:PHE327 4.3 27.9 1.0
CD2 A:LEU173 4.3 31.0 1.0
O A:HOH525 4.3 29.0 1.0
C5 A:8NE401 4.3 40.6 0.9
C1 A:8NE401 4.4 40.6 0.9
HA3 A:GLY50 4.4 31.4 1.0
HD11 A:LEU173 4.5 40.7 1.0
HD23 A:LEU173 4.6 37.2 1.0
OE1 A:GLU127 4.8 24.0 1.0
HD22 A:LEU173 4.8 37.2 1.0
OG1 A:THR183 4.8 42.6 1.0
HG21 A:VAL57 4.8 34.6 1.0
C6 A:8NE401 4.9 36.9 0.9
HA A:ASN171 4.9 14.9 1.0
O A:LEU49 4.9 26.0 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 11:55:10 2024

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