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Fluorine in PDB 7g75: Crystal Structure of Rat Autotaxin in Complex with 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-4- (Trifluoromethoxy)Benzamide, I.E. Smiles C1C(C(Cc(C1)C(=O)N) C1CC(C(CC1OCC1=Nnc(=O)N1C)C)Cl)Oc(F)(F)F with IC50=0.187764 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-4- (Trifluoromethoxy)Benzamide, I.E. Smiles C1C(C(Cc(C1)C(=O)N) C1CC(C(CC1OCC1=Nnc(=O)N1C)C)Cl)Oc(F)(F)F with IC50=0.187764 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-4- (Trifluoromethoxy)Benzamide, I.E. Smiles C1C(C(Cc(C1)C(=O)N) C1CC(C(CC1OCC1=Nnc(=O)N1C)C)Cl)Oc(F)(F)F with IC50=0.187764 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-4- (Trifluoromethoxy)Benzamide, I.E. Smiles C1C(C(Cc(C1)C(=O)N) C1CC(C(CC1OCC1=Nnc(=O)N1C)C)Cl)Oc(F)(F)F with IC50=0.187764 Microm, PDB code: 7g75 was solved by M.Stihle, J.Benz, D.Hunziker, H.Kuhne, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.78 / 1.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.092, 91.569, 119.971, 90, 90, 90
R / Rfree (%) 18.9 / 22.2

Other elements in 7g75:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-4- (Trifluoromethoxy)Benzamide, I.E. Smiles C1C(C(Cc(C1)C(=O)N) C1CC(C(CC1OCC1=Nnc(=O)N1C)C)Cl)Oc(F)(F)F with IC50=0.187764 Microm also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Sodium (Na) 1 atom
Chlorine (Cl) 2 atoms
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 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-4- (Trifluoromethoxy)Benzamide, I.E. Smiles C1C(C(Cc(C1)C(=O)N) C1CC(C(CC1OCC1=Nnc(=O)N1C)C)Cl)Oc(F)(F)F with IC50=0.187764 Microm (pdb code 7g75). 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 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-4- (Trifluoromethoxy)Benzamide, I.E. Smiles C1C(C(Cc(C1)C(=O)N) C1CC(C(CC1OCC1=Nnc(=O)N1C)C)Cl)Oc(F)(F)F with IC50=0.187764 Microm, PDB code: 7g75:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g75

Go back to Fluorine Binding Sites List in 7g75
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-4- (Trifluoromethoxy)Benzamide, I.E. Smiles C1C(C(Cc(C1)C(=O)N) C1CC(C(CC1OCC1=Nnc(=O)N1C)C)Cl)Oc(F)(F)F with IC50=0.187764 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 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-4- (Trifluoromethoxy)Benzamide, I.E. Smiles C1C(C(Cc(C1)C(=O)N) C1CC(C(CC1OCC1=Nnc(=O)N1C)C)Cl)Oc(F)(F)F with IC50=0.187764 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:28.1
occ:1.00
 F18 A:Y2Z902 0.0 28.1 1.0
C17 A:Y2Z902 1.3 28.3 1.0
F20 A:Y2Z902 2.1 31.1 1.0
O16 A:Y2Z902 2.2 25.1 1.0
F19 A:Y2Z902 2.2 28.1 1.0
CB A:LEU213 3.3 15.6 1.0
CD1 A:LEU213 3.4 18.6 1.0
CA A:PHE210 3.4 16.1 1.0
C2 A:Y2Z902 3.5 26.2 1.0
CG A:PHE210 3.6 21.5 1.0
CD1 A:PHE210 3.8 23.1 1.0
O A:PHE210 3.8 16.0 1.0
CG A:LEU213 3.9 17.6 1.0
CD2 A:PHE210 3.9 25.9 1.0
C30 A:Y2Z902 3.9 20.9 1.0
O A:THR209 4.0 16.2 1.0
CB A:PHE210 4.0 17.1 1.0
C A:PHE210 4.1 15.0 1.0
CE1 A:PHE210 4.1 26.6 1.0
CE2 A:PHE210 4.2 27.9 1.0
N A:PHE210 4.2 16.3 1.0
C1 A:Y2Z902 4.3 27.3 1.0
CA A:LEU213 4.3 14.7 1.0
CZ A:PHE210 4.3 25.5 1.0
N A:TYR214 4.4 12.4 1.0
C A:THR209 4.4 16.0 1.0
C3 A:Y2Z902 4.4 21.8 1.0
C12 A:Y2Z902 4.5 20.3 1.0
O13 A:Y2Z902 4.5 22.6 1.0
C A:LEU213 4.6 13.4 1.0
C11 A:Y2Z902 4.7 20.6 1.0
N A:LEU213 4.7 13.5 1.0
CG2 A:THR209 4.8 19.9 1.0

Fluorine binding site 2 out of 3 in 7g75

Go back to Fluorine Binding Sites List in 7g75
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-4- (Trifluoromethoxy)Benzamide, I.E. Smiles C1C(C(Cc(C1)C(=O)N) C1CC(C(CC1OCC1=Nnc(=O)N1C)C)Cl)Oc(F)(F)F with IC50=0.187764 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 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-4- (Trifluoromethoxy)Benzamide, I.E. Smiles C1C(C(Cc(C1)C(=O)N) C1CC(C(CC1OCC1=Nnc(=O)N1C)C)Cl)Oc(F)(F)F with IC50=0.187764 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:28.1
occ:1.00
 F19 A:Y2Z902 0.0 28.1 1.0
C17 A:Y2Z902 1.4 28.3 1.0
O16 A:Y2Z902 2.0 25.1 1.0
F20 A:Y2Z902 2.1 31.1 1.0
F18 A:Y2Z902 2.2 28.1 1.0
C2 A:Y2Z902 2.7 26.2 1.0
C3 A:Y2Z902 3.2 21.8 1.0
C12 A:Y2Z902 3.3 20.3 1.0
CB A:LEU213 3.4 15.6 1.0
N A:TYR214 3.4 12.4 1.0
C7 A:Y2Z902 3.5 18.5 1.0
C A:LEU213 3.6 13.4 1.0
C1 A:Y2Z902 3.6 27.3 1.0
CA A:TYR214 3.8 13.0 1.0
CB A:TYR214 3.8 14.2 1.0
O A:LEU213 4.0 13.3 1.0
CA A:LEU213 4.0 14.7 1.0
C11 A:Y2Z902 4.1 20.6 1.0
O A:PHE210 4.1 16.0 1.0
CD1 A:TYR214 4.2 16.9 1.0
C4 A:Y2Z902 4.4 21.5 1.0
CZ3 A:TRP254 4.5 19.5 1.0
CG A:TYR214 4.5 14.7 1.0
C8 A:Y2Z902 4.5 17.9 1.0
O13 A:Y2Z902 4.5 22.6 1.0
CD1 A:LEU213 4.5 18.6 1.0
CG A:LEU213 4.6 17.6 1.0
C6 A:Y2Z902 4.6 27.5 1.0
N A:LEU213 4.9 13.5 1.0
CH2 A:TRP254 4.9 21.9 1.0
CA A:PHE210 4.9 16.1 1.0
C A:PHE210 5.0 15.0 1.0
C10 A:Y2Z902 5.0 21.0 1.0
C5 A:Y2Z902 5.0 24.8 1.0

Fluorine binding site 3 out of 3 in 7g75

Go back to Fluorine Binding Sites List in 7g75
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-4- (Trifluoromethoxy)Benzamide, I.E. Smiles C1C(C(Cc(C1)C(=O)N) C1CC(C(CC1OCC1=Nnc(=O)N1C)C)Cl)Oc(F)(F)F with IC50=0.187764 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 3-[5-Chloro-4- Methyl-2-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3-Yl)Methoxy]Phenyl]-4- (Trifluoromethoxy)Benzamide, I.E. Smiles C1C(C(Cc(C1)C(=O)N) C1CC(C(CC1OCC1=Nnc(=O)N1C)C)Cl)Oc(F)(F)F with IC50=0.187764 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:31.1
occ:1.00
 F20 A:Y2Z902 0.0 31.1 1.0
C17 A:Y2Z902 1.3 28.3 1.0
F19 A:Y2Z902 2.1 28.1 1.0
F18 A:Y2Z902 2.1 28.1 1.0
O16 A:Y2Z902 2.2 25.1 1.0
C2 A:Y2Z902 2.8 26.2 1.0
C1 A:Y2Z902 3.0 27.3 1.0
CH2 A:TRP254 3.2 21.9 1.0
CD2 A:PHE210 3.3 25.9 1.0
CZ3 A:TRP254 3.3 19.5 1.0
CE2 A:PHE210 3.6 27.9 1.0
CG A:PHE210 3.8 21.5 1.0
C3 A:Y2Z902 4.0 21.8 1.0
O A:PHE210 4.2 16.0 1.0
CB A:PHE210 4.2 17.1 1.0
C6 A:Y2Z902 4.3 27.5 1.0
CA A:PHE210 4.3 16.1 1.0
CZ A:PHE210 4.4 25.5 1.0
CD1 A:PHE210 4.5 23.1 1.0
CB A:TYR214 4.5 14.2 1.0
CZ2 A:TRP254 4.5 21.3 1.0
CE3 A:TRP254 4.6 21.0 1.0
C12 A:Y2Z902 4.7 20.3 1.0
C A:PHE210 4.7 15.0 1.0
CE1 A:PHE210 4.8 26.6 1.0
N A:TYR214 4.8 12.4 1.0
CD1 A:TYR214 4.9 16.9 1.0
CB A:LEU213 4.9 15.6 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 18:05:15 2025

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