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Fluorine in PDB 7g4d: Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm, PDB code: 7g4d 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) 46.23 / 2.18
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.151, 92.454, 120.601, 90, 90, 90
R / Rfree (%) 22.6 / 28.2

Other elements in 7g4d:

The structure of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Chlorine (Cl) 4 atoms
Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm (pdb code 7g4d). 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-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm, PDB code: 7g4d:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g4d

Go back to Fluorine Binding Sites List in 7g4d
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 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-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:32.7
occ:1.00
 F27 A:Y9C901 0.0 32.7 1.0
C26 A:Y9C901 1.3 32.7 1.0
F28 A:Y9C901 2.1 31.6 1.0
O25 A:Y9C901 2.1 31.0 1.0
F29 A:Y9C901 2.2 36.1 1.0
C22 A:Y9C901 2.6 33.7 1.0
C21 A:Y9C901 2.6 33.6 1.0
CE2 A:PHE273 3.4 37.6 1.0
CD1 A:ILE167 3.5 26.4 1.0
CD2 A:PHE273 3.5 39.0 1.0
C23 A:Y9C901 3.8 33.8 1.0
CG2 A:ILE167 3.8 24.5 1.0
C20 A:Y9C901 3.9 34.1 1.0
CB A:ILE167 4.0 24.1 1.0
CG1 A:ILE167 4.3 24.3 1.0
CB A:ALA304 4.3 24.7 1.0
CZ A:PHE273 4.6 35.9 1.0
CG A:PHE273 4.7 39.5 1.0
C24 A:Y9C901 4.7 34.3 1.0
C19 A:Y9C901 4.8 32.8 1.0

Fluorine binding site 2 out of 3 in 7g4d

Go back to Fluorine Binding Sites List in 7g4d
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 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-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:31.6
occ:1.00
 F28 A:Y9C901 0.0 31.6 1.0
C26 A:Y9C901 1.3 32.7 1.0
O25 A:Y9C901 2.1 31.0 1.0
F29 A:Y9C901 2.1 36.1 1.0
F27 A:Y9C901 2.1 32.7 1.0
C22 A:Y9C901 2.8 33.7 1.0
CB A:ALA217 3.1 18.5 1.0
C23 A:Y9C901 3.4 33.8 1.0
CA A:ALA217 3.4 19.7 1.0
N A:ALA217 3.7 20.0 1.0
C21 A:Y9C901 3.8 33.6 1.0
CD2 A:PHE273 4.0 39.0 1.0
CE2 A:PHE273 4.0 37.6 1.0
C A:LEU216 4.2 20.3 1.0
O A:LEU213 4.3 20.3 1.0
CZ3 A:TRP260 4.4 25.2 1.0
O A:LEU216 4.4 22.8 1.0
C24 A:Y9C901 4.6 34.3 1.0
CB A:LEU216 4.6 22.3 1.0
C20 A:Y9C901 4.9 34.1 1.0
C A:ALA217 4.9 19.1 1.0
CE3 A:TRP260 4.9 24.8 1.0
CE A:MET512 4.9 30.0 1.0

Fluorine binding site 3 out of 3 in 7g4d

Go back to Fluorine Binding Sites List in 7g4d
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 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-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:36.1
occ:1.00
 F29 A:Y9C901 0.0 36.1 1.0
C26 A:Y9C901 1.3 32.7 1.0
F28 A:Y9C901 2.1 31.6 1.0
O25 A:Y9C901 2.1 31.0 1.0
F27 A:Y9C901 2.2 32.7 1.0
C22 A:Y9C901 3.4 33.7 1.0
CE A:MET512 3.7 30.0 1.0
CB A:LEU216 3.7 22.3 1.0
O A:LEU216 3.8 22.8 1.0
C A:LEU216 3.8 20.3 1.0
N A:ALA217 4.1 20.0 1.0
C21 A:Y9C901 4.1 33.6 1.0
CD1 A:ILE167 4.2 26.4 1.0
SD A:MET512 4.2 32.6 1.0
CG2 A:ILE167 4.2 24.5 1.0
CA A:ALA217 4.2 19.7 1.0
C23 A:Y9C901 4.4 33.8 1.0
CA A:LEU216 4.4 19.9 1.0
CB A:ALA217 4.6 18.5 1.0
CG A:LEU216 4.7 23.9 1.0
CD1 A:LEU216 4.8 25.0 1.0
CG1 A:ILE167 4.9 24.3 1.0
O A:LEU213 4.9 20.3 1.0
CB A:ILE167 5.0 24.1 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 19:57:36 2025

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