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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:

Zinc (Zn) 1 atom
Calcium (Ca) 2 atoms
Sodium (Na) 2 atoms

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

Go back to 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

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: Tue Jul 15 20:03:43 2025

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