Fluorine in PDB 7g6a: Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm
Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm
All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm:
3.1.4.39;
Protein crystallography data
The structure of Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm, PDB code: 7g6a
was solved by
M.Stihle,
J.Benz,
D.Hunziker,
M.G.Rudolph,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.67 /
1.63
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
83.657,
91.334,
118.662,
90,
90,
90
|
R / Rfree (%)
|
19.2 /
22
|
Other elements in 7g6a:
The structure of Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm
(pdb code 7g6a). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm, PDB code: 7g6a:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 7g6a
Go back to
Fluorine Binding Sites List in 7g6a
Fluorine binding site 1 out
of 6 in the Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm
 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 Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F902
b:42.5
occ:1.00
|
F23
|
A:XW2902
|
0.0
|
42.5
|
1.0
|
C7
|
A:XW2902
|
1.3
|
37.8
|
1.0
|
F24
|
A:XW2902
|
2.1
|
40.0
|
1.0
|
F25
|
A:XW2902
|
2.1
|
40.3
|
1.0
|
C10
|
A:XW2902
|
2.4
|
35.3
|
1.0
|
C17
|
A:XW2902
|
3.0
|
29.6
|
1.0
|
C14
|
A:XW2902
|
3.4
|
33.5
|
1.0
|
OG
|
A:SER169
|
3.6
|
19.3
|
1.0
|
CB
|
A:SER169
|
3.6
|
16.8
|
1.0
|
CD2
|
A:LEU213
|
3.8
|
17.9
|
1.0
|
C16
|
A:XW2902
|
4.2
|
30.0
|
1.0
|
CG2
|
A:ILE167
|
4.4
|
14.6
|
1.0
|
CD1
|
A:LEU216
|
4.4
|
17.9
|
1.0
|
C11
|
A:XW2902
|
4.6
|
33.6
|
1.0
|
CG
|
A:LEU213
|
4.7
|
16.5
|
1.0
|
CB
|
A:LEU213
|
4.7
|
17.2
|
1.0
|
CB
|
A:LEU216
|
4.8
|
14.4
|
1.0
|
O
|
A:LEU213
|
4.8
|
13.9
|
1.0
|
C18
|
A:XW2902
|
5.0
|
29.8
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 7g6a
Go back to
Fluorine Binding Sites List in 7g6a
Fluorine binding site 2 out
of 6 in the Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm
 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 Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F902
b:40.0
occ:1.00
|
F24
|
A:XW2902
|
0.0
|
40.0
|
1.0
|
C7
|
A:XW2902
|
1.3
|
37.8
|
1.0
|
F23
|
A:XW2902
|
2.1
|
42.5
|
1.0
|
F25
|
A:XW2902
|
2.1
|
40.3
|
1.0
|
C10
|
A:XW2902
|
2.4
|
35.3
|
1.0
|
C17
|
A:XW2902
|
2.9
|
29.6
|
1.0
|
CB
|
A:ALA304
|
3.5
|
14.2
|
1.0
|
C14
|
A:XW2902
|
3.7
|
33.5
|
1.0
|
CD2
|
A:PHE273
|
3.7
|
25.7
|
1.0
|
CG2
|
A:ILE167
|
4.1
|
14.6
|
1.0
|
OG
|
A:SER169
|
4.2
|
19.3
|
1.0
|
C16
|
A:XW2902
|
4.2
|
30.0
|
1.0
|
CE2
|
A:PHE273
|
4.2
|
27.0
|
1.0
|
CB
|
A:SER169
|
4.6
|
16.8
|
1.0
|
CB
|
A:ILE167
|
4.6
|
14.6
|
1.0
|
CG
|
A:PHE273
|
4.6
|
26.8
|
1.0
|
CA
|
A:ALA304
|
4.7
|
13.3
|
1.0
|
CD1
|
A:ILE167
|
4.8
|
16.4
|
1.0
|
C11
|
A:XW2902
|
4.8
|
33.6
|
1.0
|
CB
|
A:PHE273
|
4.9
|
28.4
|
1.0
|
O
|
A:PHE305
|
5.0
|
14.3
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 7g6a
Go back to
Fluorine Binding Sites List in 7g6a
Fluorine binding site 3 out
of 6 in the Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm
 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 Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F902
b:40.3
occ:1.00
|
F25
|
A:XW2902
|
0.0
|
40.3
|
1.0
|
C7
|
A:XW2902
|
1.3
|
37.8
|
1.0
|
F23
|
A:XW2902
|
2.1
|
42.5
|
1.0
|
F24
|
A:XW2902
|
2.1
|
40.0
|
1.0
|
C10
|
A:XW2902
|
2.4
|
35.3
|
1.0
|
C14
|
A:XW2902
|
2.9
|
33.5
|
1.0
|
C17
|
A:XW2902
|
3.6
|
29.6
|
1.0
|
O
|
A:LEU213
|
4.1
|
13.9
|
1.0
|
CD2
|
A:PHE273
|
4.2
|
25.7
|
1.0
|
C11
|
A:XW2902
|
4.3
|
33.6
|
1.0
|
CB
|
A:LEU216
|
4.4
|
14.4
|
1.0
|
CB
|
A:ALA217
|
4.4
|
14.6
|
1.0
|
CE2
|
A:PHE273
|
4.4
|
27.0
|
1.0
|
N
|
A:ALA217
|
4.5
|
13.0
|
1.0
|
CA
|
A:ALA217
|
4.7
|
13.2
|
1.0
|
C16
|
A:XW2902
|
4.7
|
30.0
|
1.0
|
CG2
|
A:ILE167
|
4.8
|
14.6
|
1.0
|
C
|
A:LEU216
|
5.0
|
14.5
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 7g6a
Go back to
Fluorine Binding Sites List in 7g6a
Fluorine binding site 4 out
of 6 in the Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F902
b:38.7
occ:1.00
|
F26
|
A:XW2902
|
0.0
|
38.7
|
1.0
|
C8
|
A:XW2902
|
1.4
|
36.8
|
1.0
|
F27
|
A:XW2902
|
2.1
|
32.5
|
1.0
|
F28
|
A:XW2902
|
2.2
|
34.9
|
1.0
|
C11
|
A:XW2902
|
2.5
|
33.6
|
1.0
|
C18
|
A:XW2902
|
2.8
|
29.8
|
1.0
|
CE1
|
A:PHE210
|
3.4
|
34.4
|
1.0
|
CD1
|
A:PHE210
|
3.4
|
31.1
|
1.0
|
CE2
|
A:PHE274
|
3.6
|
51.3
|
1.0
|
C14
|
A:XW2902
|
3.8
|
33.5
|
1.0
|
CZ3
|
A:TRP254
|
4.0
|
20.2
|
1.0
|
CZ
|
A:PHE274
|
4.1
|
50.5
|
1.0
|
CH2
|
A:TRP254
|
4.1
|
20.2
|
1.0
|
CB
|
A:LEU213
|
4.1
|
17.2
|
1.0
|
C16
|
A:XW2902
|
4.2
|
30.0
|
1.0
|
CD1
|
A:LEU213
|
4.5
|
18.4
|
1.0
|
N
|
A:TYR214
|
4.6
|
12.7
|
1.0
|
CD2
|
A:PHE274
|
4.6
|
48.0
|
1.0
|
CZ
|
A:PHE210
|
4.7
|
34.5
|
1.0
|
C
|
A:LEU213
|
4.7
|
12.8
|
1.0
|
N6
|
A:XW2902
|
4.7
|
26.5
|
1.0
|
CG
|
A:PHE210
|
4.8
|
26.4
|
1.0
|
CD1
|
A:TYR214
|
4.9
|
15.8
|
1.0
|
C10
|
A:XW2902
|
4.9
|
35.3
|
1.0
|
CB
|
A:TYR214
|
4.9
|
13.9
|
1.0
|
O
|
A:PHE210
|
4.9
|
14.1
|
1.0
|
CA
|
A:TYR214
|
5.0
|
13.0
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 7g6a
Go back to
Fluorine Binding Sites List in 7g6a
Fluorine binding site 5 out
of 6 in the Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F902
b:32.5
occ:1.00
|
F27
|
A:XW2902
|
0.0
|
32.5
|
1.0
|
C8
|
A:XW2902
|
1.3
|
36.8
|
1.0
|
F26
|
A:XW2902
|
2.1
|
38.7
|
1.0
|
F28
|
A:XW2902
|
2.2
|
34.9
|
1.0
|
C11
|
A:XW2902
|
2.3
|
33.6
|
1.0
|
C14
|
A:XW2902
|
2.9
|
33.5
|
1.0
|
N
|
A:TYR214
|
3.0
|
12.7
|
1.0
|
C
|
A:LEU213
|
3.0
|
12.8
|
1.0
|
O
|
A:LEU213
|
3.2
|
13.9
|
1.0
|
CA
|
A:TYR214
|
3.2
|
13.0
|
1.0
|
CB
|
A:LEU213
|
3.4
|
17.2
|
1.0
|
C18
|
A:XW2902
|
3.5
|
29.8
|
1.0
|
CB
|
A:TYR214
|
3.6
|
13.9
|
1.0
|
CD1
|
A:TYR214
|
3.7
|
15.8
|
1.0
|
CA
|
A:LEU213
|
3.8
|
14.2
|
1.0
|
CG
|
A:TYR214
|
4.1
|
15.1
|
1.0
|
C10
|
A:XW2902
|
4.2
|
35.3
|
1.0
|
O
|
A:PHE210
|
4.4
|
14.1
|
1.0
|
CZ3
|
A:TRP254
|
4.5
|
20.2
|
1.0
|
C
|
A:TYR214
|
4.6
|
13.7
|
1.0
|
C16
|
A:XW2902
|
4.6
|
30.0
|
1.0
|
CB
|
A:ALA217
|
4.7
|
14.6
|
1.0
|
CG
|
A:LEU213
|
4.8
|
16.5
|
1.0
|
N
|
A:LEU213
|
4.8
|
13.1
|
1.0
|
CD1
|
A:LEU213
|
4.8
|
18.4
|
1.0
|
CD1
|
A:PHE210
|
4.8
|
31.1
|
1.0
|
CE1
|
A:TYR214
|
4.8
|
16.5
|
1.0
|
CZ
|
A:PHE274
|
4.9
|
50.5
|
1.0
|
C17
|
A:XW2902
|
5.0
|
29.6
|
1.0
|
CH2
|
A:TRP260
|
5.0
|
17.8
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 7g6a
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Fluorine Binding Sites List in 7g6a
Fluorine binding site 6 out
of 6 in the Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm
 Mono view
 Stereo pair view
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A full contact list of Fluorine with other atoms in the F binding
site number 6 of Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F902
b:34.9
occ:1.00
|
F28
|
A:XW2902
|
0.0
|
34.9
|
1.0
|
C8
|
A:XW2902
|
1.4
|
36.8
|
1.0
|
F27
|
A:XW2902
|
2.2
|
32.5
|
1.0
|
F26
|
A:XW2902
|
2.2
|
38.7
|
1.0
|
C11
|
A:XW2902
|
2.4
|
33.6
|
1.0
|
CZ
|
A:PHE274
|
2.8
|
50.5
|
1.0
|
CE2
|
A:PHE274
|
3.2
|
51.3
|
1.0
|
C18
|
A:XW2902
|
3.3
|
29.8
|
1.0
|
C14
|
A:XW2902
|
3.3
|
33.5
|
1.0
|
CH2
|
A:TRP260
|
3.4
|
17.8
|
1.0
|
CD1
|
A:TYR214
|
3.8
|
15.8
|
1.0
|
CE1
|
A:PHE274
|
3.9
|
51.0
|
1.0
|
CZ3
|
A:TRP260
|
4.1
|
17.9
|
1.0
|
CZ3
|
A:TRP254
|
4.2
|
20.2
|
1.0
|
CZ2
|
A:TRP260
|
4.4
|
18.8
|
1.0
|
CE1
|
A:TYR214
|
4.4
|
16.5
|
1.0
|
CD2
|
A:PHE274
|
4.5
|
48.0
|
1.0
|
C16
|
A:XW2902
|
4.5
|
30.0
|
1.0
|
C10
|
A:XW2902
|
4.6
|
35.3
|
1.0
|
CH2
|
A:TRP254
|
4.8
|
20.2
|
1.0
|
CG
|
A:TYR214
|
4.8
|
15.1
|
1.0
|
CE3
|
A:TRP254
|
4.9
|
19.1
|
1.0
|
CA
|
A:TYR214
|
4.9
|
13.0
|
1.0
|
CD1
|
A:PHE274
|
5.0
|
46.1
|
1.0
|
CB
|
A:TYR214
|
5.0
|
13.9
|
1.0
|
|
Reference:
D.Hunziker,
S.C.Joachim,
C.Ullmer,
M.G.Rudolph.
Crystal Structure of A Rat Autotaxin Complex To Be Published.
Page generated: Sat Feb 8 18:05:14 2025
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