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Fluorine in PDB 7g4p: Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 Microm, PDB code: 7g4p 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) 46.72 / 2.12
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.786, 93.362, 120.964, 90, 90, 90
R / Rfree (%) 21.8 / 25.8

Other elements in 7g4p:

The structure of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 Microm also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 Microm (pdb code 7g4p). 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 Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 Microm, PDB code: 7g4p:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g4p

Go back to Fluorine Binding Sites List in 7g4p
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 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 Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:47.0
occ:1.00
 F36 A:Y6R901 0.0 47.0 1.0
C35 A:Y6R901 1.3 47.8 1.0
F37 A:Y6R901 2.2 49.4 1.0
F38 A:Y6R901 2.2 48.4 1.0
O34 A:Y6R901 2.2 46.9 1.0
C31 A:Y6R901 3.4 45.3 1.0
C A:LEU216 3.5 26.0 1.0
O A:LEU216 3.5 25.1 1.0
CB A:LEU216 3.5 27.2 1.0
CE A:MET512 3.6 30.4 1.0
N A:ALA217 3.7 26.0 1.0
CA A:ALA217 3.8 26.8 1.0
SD A:MET512 4.1 32.9 1.0
CA A:LEU216 4.2 26.2 1.0
C30 A:Y6R901 4.3 44.4 1.0
CB A:ALA217 4.3 25.0 1.0
C32 A:Y6R901 4.3 43.6 1.0
CD1 A:ILE167 4.4 32.4 1.0
CG2 A:ILE167 4.5 31.8 1.0
CG A:LEU216 4.6 30.4 1.0
O A:LEU213 4.7 25.4 1.0
CD1 A:LEU216 4.8 30.3 1.0
CG1 A:ILE167 5.0 33.4 1.0

Fluorine binding site 2 out of 3 in 7g4p

Go back to Fluorine Binding Sites List in 7g4p
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 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 Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:49.4
occ:1.00
 F37 A:Y6R901 0.0 49.4 1.0
C35 A:Y6R901 1.3 47.8 1.0
F36 A:Y6R901 2.2 47.0 1.0
F38 A:Y6R901 2.2 48.4 1.0
O34 A:Y6R901 2.2 46.9 1.0
C31 A:Y6R901 2.8 45.3 1.0
C32 A:Y6R901 3.1 43.6 1.0
CE2 A:PHE273 3.3 40.7 1.0
CD1 A:ILE167 3.4 32.4 1.0
CD2 A:PHE273 3.5 42.6 1.0
CG2 A:ILE167 3.6 31.8 1.0
C30 A:Y6R901 3.9 44.4 1.0
CB A:ILE167 4.0 32.1 1.0
CG1 A:ILE167 4.1 33.4 1.0
C33 A:Y6R901 4.3 42.3 1.0
CZ A:PHE273 4.5 36.3 1.0
CB A:ALA304 4.6 37.6 1.0
CG A:PHE273 4.8 43.9 1.0
C29 A:Y6R901 4.9 43.1 1.0
SD A:MET512 4.9 32.9 1.0
CE A:MET512 5.0 30.4 1.0

Fluorine binding site 3 out of 3 in 7g4p

Go back to Fluorine Binding Sites List in 7g4p
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 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 Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:48.4
occ:1.00
 F38 A:Y6R901 0.0 48.4 1.0
C35 A:Y6R901 1.3 47.8 1.0
F37 A:Y6R901 2.2 49.4 1.0
F36 A:Y6R901 2.2 47.0 1.0
O34 A:Y6R901 2.2 46.9 1.0
C31 A:Y6R901 2.7 45.3 1.0
C30 A:Y6R901 3.0 44.4 1.0
CB A:ALA217 3.1 25.0 1.0
CA A:ALA217 3.4 26.8 1.0
N A:ALA217 3.7 26.0 1.0
C32 A:Y6R901 3.7 43.6 1.0
CD2 A:PHE273 4.0 42.6 1.0
CZ3 A:TRP260 4.0 32.5 1.0
CE2 A:PHE273 4.1 40.7 1.0
O A:LEU213 4.1 25.4 1.0
C29 A:Y6R901 4.1 43.1 1.0
C A:LEU216 4.3 26.0 1.0
O A:LEU216 4.6 25.1 1.0
CB A:LEU216 4.6 27.2 1.0
CE3 A:TRP260 4.7 31.2 1.0
C33 A:Y6R901 4.7 42.3 1.0
C A:ALA217 4.8 26.9 1.0
C28 A:Y6R901 4.9 41.5 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 19:58:55 2025

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