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Fluorine in PDB 7g55: Crystal Structure of Rat Autotaxin in Complex with [3-Chloro-5- (Trifluoromethoxy)Phenyl]Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1CC(Cc(C1)Cl)Oc(F)(F)F with IC50=0.00942633 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [3-Chloro-5- (Trifluoromethoxy)Phenyl]Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1CC(Cc(C1)Cl)Oc(F)(F)F with IC50=0.00942633 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [3-Chloro-5- (Trifluoromethoxy)Phenyl]Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1CC(Cc(C1)Cl)Oc(F)(F)F with IC50=0.00942633 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [3-Chloro-5- (Trifluoromethoxy)Phenyl]Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1CC(Cc(C1)Cl)Oc(F)(F)F with IC50=0.00942633 Microm, PDB code: 7g55 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) 46.02 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.022, 92.042, 120.659, 90, 90, 90
R / Rfree (%) 19 / 23.5

Other elements in 7g55:

The structure of Crystal Structure of Rat Autotaxin in Complex with [3-Chloro-5- (Trifluoromethoxy)Phenyl]Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1CC(Cc(C1)Cl)Oc(F)(F)F with IC50=0.00942633 Microm also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with [3-Chloro-5- (Trifluoromethoxy)Phenyl]Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1CC(Cc(C1)Cl)Oc(F)(F)F with IC50=0.00942633 Microm (pdb code 7g55). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Rat Autotaxin in Complex with [3-Chloro-5- (Trifluoromethoxy)Phenyl]Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1CC(Cc(C1)Cl)Oc(F)(F)F with IC50=0.00942633 Microm, PDB code: 7g55:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g55

Go back to Fluorine Binding Sites List in 7g55
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [3-Chloro-5- (Trifluoromethoxy)Phenyl]Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1CC(Cc(C1)Cl)Oc(F)(F)F with IC50=0.00942633 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-Chloro-5- (Trifluoromethoxy)Phenyl]Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1CC(Cc(C1)Cl)Oc(F)(F)F with IC50=0.00942633 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:42.4
occ:1.00
 F33 A:Y68902 0.0 42.4 1.0
C32 A:Y68902 1.3 44.0 1.0
F34 A:Y68902 2.1 45.0 1.0
F35 A:Y68902 2.2 48.9 1.0
O31 A:Y68902 2.2 42.1 1.0
C26 A:Y68902 2.8 40.3 1.0
C27 A:Y68902 2.8 37.6 1.0
N A:ALA217 3.6 26.0 1.0
CA A:ALA217 3.7 26.4 1.0
CB A:ALA217 3.7 25.6 1.0
CB A:LEU216 3.8 25.8 1.0
C A:LEU216 3.8 28.8 1.0
C25 A:Y68902 4.1 39.3 1.0
C28 A:Y68902 4.1 39.0 1.0
O A:LEU213 4.1 24.3 1.0
O A:LEU216 4.2 25.8 1.0
CE2 A:PHE273 4.2 31.8 1.0
CD2 A:PHE273 4.3 33.4 1.0
CA A:LEU216 4.5 24.4 1.0
CE A:MET512 4.6 28.7 1.0
CD1 A:ILE167 4.8 35.9 1.0
CL30 A:Y68902 5.0 43.9 1.0

Fluorine binding site 2 out of 3 in 7g55

Go back to Fluorine Binding Sites List in 7g55
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [3-Chloro-5- (Trifluoromethoxy)Phenyl]Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1CC(Cc(C1)Cl)Oc(F)(F)F with IC50=0.00942633 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-Chloro-5- (Trifluoromethoxy)Phenyl]Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1CC(Cc(C1)Cl)Oc(F)(F)F with IC50=0.00942633 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:45.0
occ:1.00
 F34 A:Y68902 0.0 45.0 1.0
C32 A:Y68902 1.3 44.0 1.0
F33 A:Y68902 2.1 42.4 1.0
O31 A:Y68902 2.2 42.1 1.0
F35 A:Y68902 2.2 48.9 1.0
CB A:LEU216 3.5 25.8 1.0
C26 A:Y68902 3.5 40.3 1.0
CG2 A:ILE167 3.6 28.3 1.0
CD1 A:LEU216 3.9 31.8 1.0
C27 A:Y68902 4.1 37.6 1.0
CG A:LEU216 4.1 28.7 1.0
CE A:MET512 4.4 28.7 1.0
CD1 A:ILE167 4.4 35.9 1.0
CG1 A:VAL356 4.5 25.9 1.0
C A:LEU216 4.5 28.8 1.0
CD2 A:LEU216 4.5 25.6 1.0
C25 A:Y68902 4.5 39.3 1.0
SD A:MET512 4.6 32.6 1.0
CA A:LEU216 4.6 24.4 1.0
O A:LEU216 4.6 25.8 1.0
CB A:ILE167 4.7 28.9 1.0
N A:ALA217 4.8 26.0 1.0
CG1 A:ILE167 5.0 29.6 1.0

Fluorine binding site 3 out of 3 in 7g55

Go back to Fluorine Binding Sites List in 7g55
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [3-Chloro-5- (Trifluoromethoxy)Phenyl]Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1CC(Cc(C1)Cl)Oc(F)(F)F with IC50=0.00942633 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-Chloro-5- (Trifluoromethoxy)Phenyl]Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1CC(Cc(C1)Cl)Oc(F)(F)F with IC50=0.00942633 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:48.9
occ:1.00
 F35 A:Y68902 0.0 48.9 1.0
C32 A:Y68902 1.3 44.0 1.0
F33 A:Y68902 2.2 42.4 1.0
F34 A:Y68902 2.2 45.0 1.0
O31 A:Y68902 2.2 42.1 1.0
C26 A:Y68902 3.0 40.3 1.0
CG2 A:ILE167 3.2 28.3 1.0
CD1 A:ILE167 3.3 35.9 1.0
C25 A:Y68902 3.6 39.3 1.0
CE2 A:PHE273 3.7 31.8 1.0
CB A:ILE167 3.7 28.9 1.0
C27 A:Y68902 3.8 37.6 1.0
CD2 A:PHE273 3.9 33.4 1.0
CG1 A:ILE167 4.1 29.6 1.0
CB A:ALA304 4.3 32.9 1.0
CZ A:PHE273 4.7 28.3 1.0
C24 A:Y68902 4.8 43.0 1.0
C28 A:Y68902 4.9 39.0 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: Tue Jul 15 19:59:32 2025

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