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Fluorine in PDB 7g4y: Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-2-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-2-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-2-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 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,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-2-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 Microm, PDB code: 7g4y 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) 45.82 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.948, 91.632, 119.854, 90, 90, 90
R / Rfree (%) 18.4 / 22.5

Other elements in 7g4y:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-2-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 Microm also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Sodium (Na) 1 atom
Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom
Potassium (K) 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,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-2-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 Microm (pdb code 7g4y). 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,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-2-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 Microm, PDB code: 7g4y:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g4y

Go back to Fluorine Binding Sites List in 7g4y
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-2-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 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,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-2-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:36.8
occ:1.00
 F43 A:YDE901 0.0 36.8 1.0
C42 A:YDE901 1.4 39.1 1.0
F45 A:YDE901 2.2 40.8 1.0
C35 A:YDE901 2.3 36.7 1.0
F44 A:YDE901 2.3 37.6 1.0
C36 A:YDE901 3.0 34.2 1.0
C34 A:YDE901 3.3 34.0 1.0
CB A:SER169 3.5 21.9 1.0
CG2 A:ILE167 3.8 20.6 1.0
OG A:SER169 3.8 29.0 1.0
CD1 A:LEU216 4.0 28.2 1.0
C37 A:YDE901 4.2 33.3 1.0
CD2 A:LEU213 4.3 21.9 1.0
CB A:LEU216 4.4 21.9 1.0
C33 A:YDE901 4.5 35.0 1.0
CG1 A:VAL356 4.6 19.2 1.0
CA A:SER169 4.8 19.5 1.0
C32 A:YDE901 4.8 32.9 1.0
CG A:LEU216 4.8 24.6 1.0
CB A:ILE167 4.9 20.7 1.0

Fluorine binding site 2 out of 3 in 7g4y

Go back to Fluorine Binding Sites List in 7g4y
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-2-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 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,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-2-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:37.6
occ:1.00
 F44 A:YDE901 0.0 37.6 1.0
C42 A:YDE901 1.4 39.1 1.0
F45 A:YDE901 2.3 40.8 1.0
F43 A:YDE901 2.3 36.8 1.0
C35 A:YDE901 2.4 36.7 1.0
C34 A:YDE901 2.7 34.0 1.0
OG A:SER169 3.0 29.0 1.0
CB A:SER169 3.3 21.9 1.0
CG2 A:ILE167 3.5 20.6 1.0
CB A:ALA304 3.6 26.9 1.0
O A:PHE305 3.6 22.2 1.0
C36 A:YDE901 3.7 34.2 1.0
O A:ILE167 3.9 23.7 1.0
CB A:ILE167 4.0 20.7 1.0
C33 A:YDE901 4.1 35.0 1.0
N A:SER169 4.2 19.8 1.0
CA A:SER169 4.4 19.5 1.0
CA A:ALA304 4.4 26.7 1.0
C A:ILE167 4.5 21.6 1.0
N A:PHE305 4.5 22.6 1.0
C A:PHE305 4.5 21.7 1.0
C37 A:YDE901 4.8 33.3 1.0
C A:ALA304 4.8 24.9 1.0
N29 A:YDE901 4.8 35.6 1.0
CA A:ILE167 4.9 19.1 1.0
C32 A:YDE901 4.9 32.9 1.0
CD2 A:PHE273 4.9 27.7 1.0

Fluorine binding site 3 out of 3 in 7g4y

Go back to Fluorine Binding Sites List in 7g4y
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-2-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 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,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-2-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:40.8
occ:1.00
 F45 A:YDE901 0.0 40.8 1.0
C42 A:YDE901 1.4 39.1 1.0
F43 A:YDE901 2.2 36.8 1.0
F44 A:YDE901 2.3 37.6 1.0
C35 A:YDE901 2.4 36.7 1.0
C36 A:YDE901 2.8 34.2 1.0
CG2 A:ILE167 3.4 20.6 1.0
C34 A:YDE901 3.5 34.0 1.0
CE2 A:PHE273 3.6 29.0 1.0
CD1 A:ILE167 3.7 21.6 1.0
CD2 A:PHE273 3.7 27.7 1.0
CB A:ILE167 3.9 20.7 1.0
CB A:ALA304 4.0 26.9 1.0
C37 A:YDE901 4.1 33.3 1.0
CG1 A:ILE167 4.4 20.2 1.0
C33 A:YDE901 4.6 35.0 1.0
CZ A:PHE273 4.8 27.8 1.0
C32 A:YDE901 4.9 32.9 1.0
CG A:PHE273 4.9 27.9 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 19:59:24 2025

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