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Fluorine in PDB 7g46: Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 Microm, PDB code: 7g46 was solved by M.Stihle, J.Benz, D.Hunziker, P.Mattei, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.58 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.858, 91.156, 118.324, 90, 90, 90
R / Rfree (%) 20.1 / 24.4

Other elements in 7g46:

The structure of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 Microm also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 Microm (pdb code 7g46). 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 [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 Microm, PDB code: 7g46:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g46

Go back to Fluorine Binding Sites List in 7g46
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 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 [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:44.4
occ:1.00
 F34 A:XGW901 0.0 44.4 1.0
C33 A:XGW901 1.3 44.7 1.0
F35 A:XGW901 2.1 44.0 1.0
F36 A:XGW901 2.2 46.6 1.0
O32 A:XGW901 2.3 42.8 1.0
C29 A:XGW901 2.9 40.6 1.0
CE2 A:PHE273 3.2 29.0 1.0
CD2 A:PHE273 3.3 28.9 1.0
C30 A:XGW901 3.5 40.0 1.0
CB A:ALA217 3.5 16.4 1.0
CA A:ALA217 3.6 17.4 1.0
C28 A:XGW901 3.7 40.3 1.0
CZ3 A:TRP260 3.9 23.2 1.0
N A:ALA217 4.1 16.7 1.0
CE3 A:TRP260 4.4 22.6 1.0
CZ A:PHE273 4.5 29.6 1.0
C31 A:XGW901 4.6 40.1 1.0
CD1 A:ILE167 4.6 23.1 1.0
CG A:PHE273 4.6 30.2 1.0
CB A:LEU259 4.7 18.3 1.0
C A:LEU216 4.7 17.6 1.0
C27 A:XGW901 4.7 39.9 1.0
CD2 A:LEU259 4.8 19.4 1.0
O A:LEU213 4.8 18.6 1.0
C A:ALA217 4.9 17.7 1.0

Fluorine binding site 2 out of 3 in 7g46

Go back to Fluorine Binding Sites List in 7g46
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 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 [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:44.0
occ:1.00
 F35 A:XGW901 0.0 44.0 1.0
C33 A:XGW901 1.3 44.7 1.0
F34 A:XGW901 2.1 44.4 1.0
F36 A:XGW901 2.2 46.6 1.0
O32 A:XGW901 2.2 42.8 1.0
N A:ALA217 3.1 16.7 1.0
C A:LEU216 3.2 17.6 1.0
CB A:LEU216 3.3 18.2 1.0
CA A:ALA217 3.4 17.4 1.0
O A:LEU216 3.5 18.5 1.0
C29 A:XGW901 3.5 40.6 1.0
CE A:MET512 3.6 21.5 1.0
CA A:LEU216 3.9 17.9 1.0
CB A:ALA217 4.0 16.4 1.0
C28 A:XGW901 4.2 40.3 1.0
SD A:MET512 4.3 24.3 1.0
O A:LEU213 4.4 18.6 1.0
C30 A:XGW901 4.5 40.0 1.0
C A:ALA217 4.7 17.7 1.0
CG A:LEU216 4.7 20.5 1.0
CD1 A:ILE167 4.7 23.1 1.0
CG2 A:ILE167 4.9 20.6 1.0
CE2 A:PHE273 5.0 29.0 1.0

Fluorine binding site 3 out of 3 in 7g46

Go back to Fluorine Binding Sites List in 7g46
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 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 [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:46.6
occ:1.00
 F36 A:XGW901 0.0 46.6 1.0
C33 A:XGW901 1.3 44.7 1.0
F34 A:XGW901 2.2 44.4 1.0
F35 A:XGW901 2.2 44.0 1.0
O32 A:XGW901 2.3 42.8 1.0
C28 A:XGW901 2.9 40.3 1.0
C29 A:XGW901 2.9 40.6 1.0
CG2 A:ILE167 3.3 20.6 1.0
CD1 A:ILE167 3.4 23.1 1.0
CE2 A:PHE273 3.7 29.0 1.0
CB A:ILE167 3.8 22.0 1.0
CG1 A:ILE167 4.0 21.2 1.0
C27 A:XGW901 4.1 39.9 1.0
CD2 A:PHE273 4.1 28.9 1.0
C30 A:XGW901 4.1 40.0 1.0
SD A:MET512 4.6 24.3 1.0
CE A:MET512 4.8 21.5 1.0
CB A:ALA304 4.9 21.2 1.0
CZ A:PHE273 5.0 29.6 1.0
CB A:LEU216 5.0 18.2 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 19:56:53 2025

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