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Fluorine in PDB 7g5r: Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, 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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, 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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, 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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, 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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm, PDB code: 7g5r 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) 48.89 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.288, 91.722, 120.027, 90, 90, 90
R / Rfree (%) 20 / 25

Other elements in 7g5r:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, 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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, 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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm (pdb code 7g5r). 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, 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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm, PDB code: 7g5r:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g5r

Go back to Fluorine Binding Sites List in 7g5r
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, 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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, 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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:44.0
occ:1.00
 F37 A:YQ9902 0.0 44.0 1.0
C36 A:YQ9902 1.3 44.0 1.0
F39 A:YQ9902 2.1 41.9 1.0
F38 A:YQ9902 2.2 43.9 1.0
C35 A:YQ9902 2.4 40.4 1.0
O34 A:YQ9902 2.6 35.9 1.0
O A:LEU213 2.9 26.2 1.0
CB A:LEU216 3.7 26.2 1.0
C A:LEU213 3.8 23.9 1.0
C33 A:YQ9902 3.9 36.4 1.0
N A:ALA217 4.0 23.6 1.0
CB A:ALA217 4.0 21.4 1.0
CA A:LEU213 4.0 24.3 1.0
CB A:LEU213 4.2 23.1 1.0
CD2 A:LEU213 4.3 25.8 1.0
CA A:ALA217 4.3 22.4 1.0
C A:LEU216 4.4 24.2 1.0
C40 A:YQ9902 4.5 36.8 1.0
CA A:LEU216 4.5 24.1 1.0
CD1 A:LEU216 4.6 31.7 1.0
C30 A:YQ9902 4.7 36.2 1.0
N32 A:YQ9902 4.7 35.0 1.0
CG A:LEU216 4.8 29.6 1.0
O A:HOH1327 4.8 24.8 1.0
CG A:LEU213 4.8 25.2 1.0
N A:TYR214 5.0 23.5 1.0

Fluorine binding site 2 out of 3 in 7g5r

Go back to Fluorine Binding Sites List in 7g5r
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, 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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, 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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:43.9
occ:1.00
 F38 A:YQ9902 0.0 43.9 1.0
C36 A:YQ9902 1.4 44.0 1.0
F37 A:YQ9902 2.2 44.0 1.0
F39 A:YQ9902 2.2 41.9 1.0
C35 A:YQ9902 2.4 40.4 1.0
O A:HOH1327 3.0 24.8 1.0
O34 A:YQ9902 3.5 35.9 1.0
CG2 A:ILE167 3.5 25.7 1.0
CB A:ILE167 4.4 27.3 1.0
CD1 A:ILE167 4.5 29.4 1.0
CB A:SER169 4.6 29.3 1.0
OG A:SER169 4.6 34.4 1.0
C33 A:YQ9902 4.7 36.4 1.0
CB A:LEU216 4.7 26.2 1.0
CE2 A:PHE273 4.7 40.6 1.0
O A:HOH1293 4.8 49.0 1.0
CD2 A:PHE273 4.8 41.1 1.0
N32 A:YQ9902 4.9 35.0 1.0
CG1 A:ILE167 5.0 27.6 1.0
O A:LEU213 5.0 26.2 1.0

Fluorine binding site 3 out of 3 in 7g5r

Go back to Fluorine Binding Sites List in 7g5r
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, 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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, 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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:41.9
occ:1.00
 F39 A:YQ9902 0.0 41.9 1.0
C36 A:YQ9902 1.4 44.0 1.0
F37 A:YQ9902 2.1 44.0 1.0
F38 A:YQ9902 2.2 43.9 1.0
C35 A:YQ9902 2.5 40.4 1.0
O34 A:YQ9902 2.8 35.9 1.0
CD2 A:PHE273 3.6 41.1 1.0
CB A:ALA217 3.6 21.4 1.0
CE2 A:PHE273 3.7 40.6 1.0
CZ3 A:TRP260 4.0 33.4 1.0
C33 A:YQ9902 4.1 36.4 1.0
CA A:ALA217 4.2 22.4 1.0
O A:LEU213 4.3 26.2 1.0
N A:ALA217 4.5 23.6 1.0
O A:HOH1327 4.6 24.8 1.0
CE3 A:TRP260 4.7 31.1 1.0
C40 A:YQ9902 4.7 36.8 1.0
N32 A:YQ9902 4.8 35.0 1.0
C30 A:YQ9902 4.9 36.2 1.0
CG A:PHE273 4.9 43.7 1.0
CH2 A:TRP260 4.9 34.8 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 17:58:11 2025

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