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Fluorine in PDB 7g64: Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 Microm, PDB code: 7g64 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) 45.88 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.38, 91.754, 121.021, 90, 90, 90
R / Rfree (%) 19.5 / 24.9

Other elements in 7g64:

The structure of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 Microm also contains other interesting chemical elements:

Sodium (Na) 1 atom
Calcium (Ca) 2 atoms
Potassium (K) 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 [(3AS,6AS)-5-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 Microm (pdb code 7g64). 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-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 Microm, PDB code: 7g64:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g64

Go back to Fluorine Binding Sites List in 7g64
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 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-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F904

b:50.0
occ:1.00
 F34 A:YDV904 0.0 50.0 1.0
C33 A:YDV904 1.3 56.9 1.0
F35 A:YDV904 2.1 57.7 1.0
F36 A:YDV904 2.2 56.4 1.0
C32 A:YDV904 2.3 48.2 1.0
O A:HOH1298 2.9 33.9 1.0
O30 A:YDV904 3.3 45.5 1.0
CB A:SER169 3.5 26.0 1.0
OG A:SER169 3.7 34.6 1.0
CG2 A:ILE167 3.8 23.7 1.0
CD2 A:LEU213 4.1 21.0 1.0
CD1 A:LEU216 4.1 33.5 1.0
CB A:LEU216 4.4 25.3 1.0
C27 A:YDV904 4.5 36.9 1.0
N28 A:YDV904 4.8 38.8 1.0
CG A:LEU216 4.9 31.7 1.0
CA A:SER169 4.9 25.7 1.0
CB A:ILE167 4.9 25.4 1.0
O A:LEU213 4.9 23.7 1.0
CG1 A:VAL356 5.0 23.9 1.0

Fluorine binding site 2 out of 3 in 7g64

Go back to Fluorine Binding Sites List in 7g64
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 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-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F904

b:57.7
occ:1.00
 F35 A:YDV904 0.0 57.7 1.0
C33 A:YDV904 1.3 56.9 1.0
F34 A:YDV904 2.1 50.0 1.0
F36 A:YDV904 2.1 56.4 1.0
C32 A:YDV904 2.3 48.2 1.0
O A:HOH1298 2.7 33.9 1.0
O30 A:YDV904 3.3 45.5 1.0
CD2 A:PHE273 3.4 41.7 1.0
CE2 A:PHE273 3.5 42.7 1.0
CG2 A:ILE167 3.7 23.7 1.0
CD1 A:ILE167 4.1 25.3 1.0
CB A:ALA304 4.2 27.8 1.0
CB A:ILE167 4.2 25.4 1.0
CG A:PHE273 4.5 43.5 1.0
C27 A:YDV904 4.5 36.9 1.0
CZ A:PHE273 4.7 35.8 1.0
CG1 A:ILE167 4.8 23.9 1.0
N28 A:YDV904 5.0 38.8 1.0

Fluorine binding site 3 out of 3 in 7g64

Go back to Fluorine Binding Sites List in 7g64
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 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-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F904

b:56.4
occ:1.00
 F36 A:YDV904 0.0 56.4 1.0
C33 A:YDV904 1.4 56.9 1.0
F35 A:YDV904 2.1 57.7 1.0
F34 A:YDV904 2.2 50.0 1.0
C32 A:YDV904 2.4 48.2 1.0
O30 A:YDV904 2.5 45.5 1.0
O A:LEU213 3.5 23.7 1.0
C27 A:YDV904 3.8 36.9 1.0
C31 A:YDV904 4.0 42.5 1.0
CB A:ALA217 4.1 22.6 1.0
CB A:LEU216 4.1 25.3 1.0
N A:ALA217 4.2 25.5 1.0
CD2 A:PHE273 4.3 41.7 1.0
O A:HOH1298 4.3 33.9 1.0
C A:LEU213 4.4 23.5 1.0
C26 A:YDV904 4.4 38.1 1.0
CA A:ALA217 4.5 24.1 1.0
CB A:LEU213 4.6 22.2 1.0
C37 A:YDV904 4.6 46.4 1.0
CA A:LEU213 4.7 25.6 1.0
C A:LEU216 4.7 27.5 1.0
CE2 A:PHE273 4.7 42.7 1.0
CD2 A:LEU213 4.7 21.0 1.0
N28 A:YDV904 4.8 38.8 1.0
CD1 A:LEU216 4.9 33.5 1.0
CA A:LEU216 5.0 23.7 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 18:00:08 2025

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