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Fluorine in PDB 7g4f: Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 Microm, PDB code: 7g4f 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) 42.87 / 2.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.087, 91.718, 119.857, 90, 90, 90
R / Rfree (%) 18.7 / 23.2

Other elements in 7g4f:

The structure of Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 Microm also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Calcium (Ca) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 Microm (pdb code 7g4f). 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 (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 Microm, PDB code: 7g4f:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g4f

Go back to Fluorine Binding Sites List in 7g4f
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 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 (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:43.9
occ:1.00
 F34 A:YNX902 0.0 43.9 1.0
C33 A:YNX902 1.3 41.2 1.0
O32 A:YNX902 2.1 43.8 1.0
F36 A:YNX902 2.2 46.7 1.0
F35 A:YNX902 2.2 42.8 1.0
C29 A:YNX902 2.7 41.8 1.0
C30 A:YNX902 3.0 39.6 1.0
CB A:LEU216 3.6 21.7 1.0
CD1 A:LEU216 3.8 24.4 1.0
C28 A:YNX902 3.8 41.1 1.0
CG2 A:ILE167 4.2 17.4 1.0
O A:LEU213 4.3 20.6 1.0
C31 A:YNX902 4.3 42.0 1.0
CG A:LEU216 4.3 22.4 1.0
CB A:SER169 4.6 21.1 1.0
CD2 A:LEU213 4.6 17.4 1.0
N A:ALA217 4.7 19.7 1.0
CA A:LEU216 4.8 20.7 1.0
C A:LEU216 4.8 20.4 1.0
C27 A:YNX902 4.9 40.1 1.0
CG1 A:VAL356 4.9 20.5 1.0
OG A:SER169 4.9 27.5 1.0
CA A:LEU213 5.0 19.3 1.0

Fluorine binding site 2 out of 3 in 7g4f

Go back to Fluorine Binding Sites List in 7g4f
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 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 (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:42.8
occ:1.00
 F35 A:YNX902 0.0 42.8 1.0
C33 A:YNX902 1.3 41.2 1.0
F36 A:YNX902 2.1 46.7 1.0
F34 A:YNX902 2.2 43.9 1.0
O32 A:YNX902 2.2 43.8 1.0
N A:ALA217 3.5 19.7 1.0
CA A:ALA217 3.5 19.5 1.0
C29 A:YNX902 3.6 41.8 1.0
C A:LEU216 3.7 20.4 1.0
CB A:LEU216 3.7 21.7 1.0
CB A:ALA217 3.9 20.0 1.0
O A:LEU216 3.9 20.2 1.0
CE A:MET512 4.0 19.7 1.0
C30 A:YNX902 4.1 39.6 1.0
CD1 A:ILE167 4.3 21.1 1.0
CA A:LEU216 4.3 20.7 1.0
SD A:MET512 4.5 24.6 1.0
CE2 A:PHE273 4.5 26.9 1.0
O A:LEU213 4.6 20.6 1.0
C28 A:YNX902 4.6 41.1 1.0
CG2 A:ILE167 4.7 17.4 1.0
CD2 A:PHE273 4.8 27.4 1.0
C A:ALA217 4.9 18.4 1.0
CG A:LEU216 4.9 22.4 1.0

Fluorine binding site 3 out of 3 in 7g4f

Go back to Fluorine Binding Sites List in 7g4f
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 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 (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:46.7
occ:1.00
 F36 A:YNX902 0.0 46.7 1.0
C33 A:YNX902 1.3 41.2 1.0
F35 A:YNX902 2.1 42.8 1.0
F34 A:YNX902 2.2 43.9 1.0
O32 A:YNX902 2.2 43.8 1.0
C30 A:YNX902 2.5 39.6 1.0
C29 A:YNX902 2.7 41.8 1.0
CG2 A:ILE167 3.4 17.4 1.0
CD1 A:ILE167 3.6 21.1 1.0
CE2 A:PHE273 3.6 26.9 1.0
CD2 A:PHE273 3.7 27.4 1.0
C31 A:YNX902 3.9 42.0 1.0
CB A:ILE167 4.0 19.0 1.0
C28 A:YNX902 4.1 41.1 1.0
CG1 A:ILE167 4.3 19.1 1.0
CB A:ALA304 4.4 20.9 1.0
CZ A:PHE273 4.8 25.4 1.0
C26 A:YNX902 5.0 37.3 1.0
CG A:PHE273 5.0 27.7 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 17:51:55 2025

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