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Fluorine in PDB 7g5u: Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 Microm, PDB code: 7g5u 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) 45.86 / 2.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.092, 91.713, 119.99, 90, 90, 90
R / Rfree (%) 20.1 / 24.1

Other elements in 7g5u:

The structure of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 Microm also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 Microm (pdb code 7g5u). 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 [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 Microm, PDB code: 7g5u:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g5u

Go back to Fluorine Binding Sites List in 7g5u
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 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 [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:30.6
occ:1.00
 F37 A:YG2901 0.0 30.6 1.0
C36 A:YG2901 1.4 34.8 1.0
F39 A:YG2901 2.2 34.9 1.0
F38 A:YG2901 2.2 36.5 1.0
C35 A:YG2901 2.4 34.1 1.0
OG A:SER169 2.9 28.8 1.0
CB A:SER169 3.3 23.7 1.0
O A:PHE305 3.4 29.1 1.0
CG2 A:ILE167 3.4 24.0 1.0
CB A:ALA304 3.5 27.9 1.0
O34 A:YG2901 3.6 34.2 1.0
O A:ILE167 3.8 28.1 1.0
CB A:ILE167 4.0 25.4 1.0
N A:SER169 4.1 23.5 1.0
C A:PHE305 4.2 27.6 1.0
CA A:ALA304 4.2 28.3 1.0
CA A:SER169 4.3 23.3 1.0
N A:PHE305 4.3 27.8 1.0
C A:ILE167 4.3 27.2 1.0
C A:ALA304 4.6 27.9 1.0
C26 A:YG2901 4.8 32.2 1.0
CA A:ILE167 4.9 24.6 1.0
N A:TYR306 4.9 26.1 1.0
O A:PHE273 5.0 41.9 1.0
C A:PHE168 5.0 24.5 1.0
CA A:PHE305 5.0 28.4 1.0

Fluorine binding site 2 out of 3 in 7g5u

Go back to Fluorine Binding Sites List in 7g5u
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 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 [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:36.5
occ:1.00
 F38 A:YG2901 0.0 36.5 1.0
C36 A:YG2901 1.3 34.8 1.0
F39 A:YG2901 2.1 34.9 1.0
F37 A:YG2901 2.2 30.6 1.0
C35 A:YG2901 2.4 34.1 1.0
O34 A:YG2901 2.6 34.2 1.0
CD2 A:PHE273 3.1 31.2 1.0
CB A:ALA304 3.4 27.9 1.0
CE2 A:PHE273 3.7 31.6 1.0
CG A:PHE273 3.9 31.5 1.0
C26 A:YG2901 4.0 32.2 1.0
CB A:PHE273 4.1 34.6 1.0
CG2 A:ILE167 4.2 24.0 1.0
O A:PHE273 4.5 41.9 1.0
C33 A:YG2901 4.5 33.8 1.0
CD1 A:ILE167 4.6 26.6 1.0
CB A:ILE167 4.6 25.4 1.0
CA A:ALA304 4.7 28.3 1.0
OG A:SER169 4.7 28.8 1.0
C28 A:YG2901 4.7 32.4 1.0
C27 A:YG2901 4.9 33.6 1.0
CZ A:PHE273 4.9 29.6 1.0
CA A:PHE273 4.9 36.2 1.0

Fluorine binding site 3 out of 3 in 7g5u

Go back to Fluorine Binding Sites List in 7g5u
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 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 [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:34.9
occ:1.00
 F39 A:YG2901 0.0 34.9 1.0
C36 A:YG2901 1.3 34.8 1.0
F38 A:YG2901 2.1 36.5 1.0
F37 A:YG2901 2.2 30.6 1.0
C35 A:YG2901 2.4 34.1 1.0
O34 A:YG2901 2.8 34.2 1.0
OG A:SER169 3.5 28.8 1.0
CB A:SER169 3.5 23.7 1.0
CG2 A:ILE167 4.0 24.0 1.0
C26 A:YG2901 4.1 32.2 1.0
CD2 A:LEU213 4.1 25.9 1.0
C33 A:YG2901 4.6 33.8 1.0
C28 A:YG2901 4.8 32.4 1.0
CD1 A:LEU216 4.8 27.6 1.0
CA A:SER169 4.9 23.3 1.0
C27 A:YG2901 5.0 33.6 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 17:58:12 2025

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