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Fluorine in PDB 7g5t: Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 Microm, PDB code: 7g5t 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) 45.72 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.799, 91.434, 119.561, 90, 90, 90
R / Rfree (%) 19.7 / 23.2

Other elements in 7g5t:

The structure of Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom
Sodium (Na) 3 atoms
Calcium (Ca) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 Microm (pdb code 7g5t). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 Microm, PDB code: 7g5t:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7g5t

Go back to Fluorine Binding Sites List in 7g5t
Fluorine binding site 1 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 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 [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:53.3
occ:1.00
 F34 A:Y6I901 0.0 53.3 1.0
C33 A:Y6I901 1.3 48.7 1.0
F35 A:Y6I901 2.1 49.4 1.0
F36 A:Y6I901 2.2 44.7 1.0
O32 A:Y6I901 2.2 43.8 1.0
C29 A:Y6I901 2.9 45.1 1.0
C30 A:Y6I901 2.9 45.1 1.0
CG2 A:ILE167 3.6 19.8 1.0
CB A:LEU216 3.7 16.9 1.0
CD1 A:LEU216 4.2 19.9 1.0
C28 A:Y6I901 4.2 45.3 1.0
C31 A:Y6I901 4.3 45.3 1.0
CG A:LEU216 4.5 18.1 1.0
CB A:ILE167 4.7 20.1 1.0
F37 A:Y6I901 4.7 54.9 1.0
C A:LEU216 4.8 17.7 1.0
O A:LEU213 4.8 17.0 1.0
CD1 A:ILE167 4.8 20.9 1.0
CB A:SER169 4.8 25.6 1.0
CG1 A:VAL356 4.8 15.4 1.0
N A:ALA217 4.9 17.0 1.0
CA A:LEU216 4.9 17.6 1.0

Fluorine binding site 2 out of 4 in 7g5t

Go back to Fluorine Binding Sites List in 7g5t
Fluorine binding site 2 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 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 [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:49.4
occ:1.00
 F35 A:Y6I901 0.0 49.4 1.0
C33 A:Y6I901 1.3 48.7 1.0
F36 A:Y6I901 2.1 44.7 1.0
F34 A:Y6I901 2.1 53.3 1.0
O32 A:Y6I901 2.3 43.8 1.0
C29 A:Y6I901 2.8 45.1 1.0
C30 A:Y6I901 3.1 45.1 1.0
CE2 A:PHE273 3.2 29.4 1.0
CD2 A:PHE273 3.4 28.1 1.0
CD1 A:ILE167 3.7 20.9 1.0
C28 A:Y6I901 3.8 45.3 1.0
CG2 A:ILE167 4.0 19.8 1.0
F37 A:Y6I901 4.2 54.9 1.0
C31 A:Y6I901 4.3 45.3 1.0
CB A:ILE167 4.4 20.1 1.0
CB A:ALA304 4.4 22.2 1.0
CZ A:PHE273 4.5 28.3 1.0
CG1 A:ILE167 4.6 19.7 1.0
CG A:PHE273 4.7 29.2 1.0
C27 A:Y6I901 4.8 46.1 1.0
CB A:ALA217 4.8 18.0 1.0
CA A:ALA217 5.0 18.0 1.0

Fluorine binding site 3 out of 4 in 7g5t

Go back to Fluorine Binding Sites List in 7g5t
Fluorine binding site 3 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 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 [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:44.7
occ:1.00
 F36 A:Y6I901 0.0 44.7 1.0
C33 A:Y6I901 1.3 48.7 1.0
F35 A:Y6I901 2.1 49.4 1.0
F34 A:Y6I901 2.2 53.3 1.0
O32 A:Y6I901 2.3 43.8 1.0
N A:ALA217 3.2 17.0 1.0
CA A:ALA217 3.3 18.0 1.0
C A:LEU216 3.3 17.7 1.0
O A:LEU216 3.5 18.1 1.0
C29 A:Y6I901 3.5 45.1 1.0
CB A:ALA217 3.6 18.0 1.0
CB A:LEU216 3.6 16.9 1.0
CE A:MET512 4.0 20.1 1.0
CA A:LEU216 4.1 17.6 1.0
O A:LEU213 4.3 17.0 1.0
C30 A:Y6I901 4.3 45.1 1.0
F37 A:Y6I901 4.4 54.9 1.0
C28 A:Y6I901 4.5 45.3 1.0
SD A:MET512 4.6 22.4 1.0
C A:ALA217 4.6 18.5 1.0
CE2 A:PHE273 4.7 29.4 1.0
CD1 A:ILE167 4.8 20.9 1.0
CG A:LEU216 4.9 18.1 1.0
CD2 A:PHE273 5.0 28.1 1.0

Fluorine binding site 4 out of 4 in 7g5t

Go back to Fluorine Binding Sites List in 7g5t
Fluorine binding site 4 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 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 [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:54.9
occ:1.00
 F37 A:Y6I901 0.0 54.9 1.0
C28 A:Y6I901 1.3 45.3 1.0
C29 A:Y6I901 2.3 45.1 1.0
C27 A:Y6I901 2.4 46.1 1.0
O32 A:Y6I901 2.5 43.8 1.0
CZ3 A:TRP260 3.5 25.9 1.0
C30 A:Y6I901 3.6 45.1 1.0
C26 A:Y6I901 3.6 47.0 1.0
O A:LEU213 3.8 17.0 1.0
CH2 A:TRP260 3.8 26.8 1.0
C33 A:Y6I901 3.8 48.7 1.0
CB A:ALA217 3.9 18.0 1.0
CZ A:PHE274 3.9 45.1 1.0
C31 A:Y6I901 4.1 45.3 1.0
F35 A:Y6I901 4.2 49.4 1.0
C A:LEU213 4.3 16.8 1.0
F36 A:Y6I901 4.4 44.7 1.0
CB A:LEU213 4.4 16.7 1.0
CE2 A:PHE274 4.4 44.1 1.0
CE1 A:PHE274 4.4 45.5 1.0
CD2 A:PHE273 4.5 28.1 1.0
CE3 A:TRP260 4.7 26.4 1.0
F34 A:Y6I901 4.7 53.3 1.0
CA A:LEU213 4.9 16.7 1.0
C25 A:Y6I901 4.9 45.1 1.0
N A:TYR214 5.0 17.0 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 17:58:11 2025

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