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Fluorine in PDB 7g3z: Crystal Structure of Rat Autotaxin in Complex with 3-(2-Fluoro-4- Methylphenyl)-N-[(5-Methylpyrazin-2-Yl)Methyl]-5-(5-Propyltetrazol-1- Yl)Benzamide, I.E. Smiles C(C1NCC(NC1)C)Nc(=O)C1CC(Cc(N2C(=Nn=N2) Ccc)C1)C1CCC(CC1F)C with IC50=0.771863 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-(2-Fluoro-4- Methylphenyl)-N-[(5-Methylpyrazin-2-Yl)Methyl]-5-(5-Propyltetrazol-1- Yl)Benzamide, I.E. Smiles C(C1NCC(NC1)C)Nc(=O)C1CC(Cc(N2C(=Nn=N2) Ccc)C1)C1CCC(CC1F)C with IC50=0.771863 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-(2-Fluoro-4- Methylphenyl)-N-[(5-Methylpyrazin-2-Yl)Methyl]-5-(5-Propyltetrazol-1- Yl)Benzamide, I.E. Smiles C(C1NCC(NC1)C)Nc(=O)C1CC(Cc(N2C(=Nn=N2) Ccc)C1)C1CCC(CC1F)C with IC50=0.771863 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-(2-Fluoro-4- Methylphenyl)-N-[(5-Methylpyrazin-2-Yl)Methyl]-5-(5-Propyltetrazol-1- Yl)Benzamide, I.E. Smiles C(C1NCC(NC1)C)Nc(=O)C1CC(Cc(N2C(=Nn=N2) Ccc)C1)C1CCC(CC1F)C with IC50=0.771863 Microm, PDB code: 7g3z was solved by M.Stihle, J.Benz, D.Hunziker, L.Hu, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.01 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.107, 92.02, 119.812, 90, 90, 90
R / Rfree (%) 19.1 / 23.1

Other elements in 7g3z:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-(2-Fluoro-4- Methylphenyl)-N-[(5-Methylpyrazin-2-Yl)Methyl]-5-(5-Propyltetrazol-1- Yl)Benzamide, I.E. Smiles C(C1NCC(NC1)C)Nc(=O)C1CC(Cc(N2C(=Nn=N2) Ccc)C1)C1CCC(CC1F)C with IC50=0.771863 Microm also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with 3-(2-Fluoro-4- Methylphenyl)-N-[(5-Methylpyrazin-2-Yl)Methyl]-5-(5-Propyltetrazol-1- Yl)Benzamide, I.E. Smiles C(C1NCC(NC1)C)Nc(=O)C1CC(Cc(N2C(=Nn=N2) Ccc)C1)C1CCC(CC1F)C with IC50=0.771863 Microm (pdb code 7g3z). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Crystal Structure of Rat Autotaxin in Complex with 3-(2-Fluoro-4- Methylphenyl)-N-[(5-Methylpyrazin-2-Yl)Methyl]-5-(5-Propyltetrazol-1- Yl)Benzamide, I.E. Smiles C(C1NCC(NC1)C)Nc(=O)C1CC(Cc(N2C(=Nn=N2) Ccc)C1)C1CCC(CC1F)C with IC50=0.771863 Microm, PDB code: 7g3z:

Fluorine binding site 1 out of 1 in 7g3z

Go back to Fluorine Binding Sites List in 7g3z
Fluorine binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with 3-(2-Fluoro-4- Methylphenyl)-N-[(5-Methylpyrazin-2-Yl)Methyl]-5-(5-Propyltetrazol-1- Yl)Benzamide, I.E. Smiles C(C1NCC(NC1)C)Nc(=O)C1CC(Cc(N2C(=Nn=N2) Ccc)C1)C1CCC(CC1F)C with IC50=0.771863 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-(2-Fluoro-4- Methylphenyl)-N-[(5-Methylpyrazin-2-Yl)Methyl]-5-(5-Propyltetrazol-1- Yl)Benzamide, I.E. Smiles C(C1NCC(NC1)C)Nc(=O)C1CC(Cc(N2C(=Nn=N2) Ccc)C1)C1CCC(CC1F)C with IC50=0.771863 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:23.9
occ:1.00
 F32 A:YLU902 0.0 23.9 1.0
C18 A:YLU902 1.3 21.6 1.0
C17 A:YLU902 2.3 20.3 1.0
C13 A:YLU902 2.4 22.1 1.0
C10 A:YLU902 2.8 23.4 1.0
C09 A:YLU902 3.0 23.8 1.0
CB A:ALA217 3.1 18.9 1.0
CA A:ALA217 3.4 19.5 1.0
CE2 A:PHE273 3.5 21.9 1.0
CZ3 A:TRP260 3.5 23.6 1.0
CD2 A:PHE273 3.6 23.2 1.0
C16 A:YLU902 3.6 21.1 1.0
C14 A:YLU902 3.7 22.4 1.0
N A:ALA217 3.7 18.5 1.0
C11 A:YLU902 4.0 23.8 1.0
C12 A:YLU902 4.1 26.3 1.0
C15 A:YLU902 4.2 21.0 1.0
O A:LEU213 4.2 20.1 1.0
C A:LEU216 4.3 20.0 1.0
CE3 A:TRP260 4.3 25.8 1.0
CH2 A:TRP260 4.5 24.2 1.0
O A:LEU216 4.6 20.2 1.0
CZ A:PHE273 4.8 25.4 1.0
C A:ALA217 4.8 19.6 1.0
C25 A:YLU902 4.8 20.7 1.0
CB A:LEU216 4.8 19.3 1.0
CG A:PHE273 4.8 25.6 1.0
C19 A:YLU902 4.9 27.8 1.0
C22 A:YLU902 4.9 26.1 1.0
O20 A:YLU902 4.9 27.4 1.0
C21 A:YLU902 5.0 25.5 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 17:51:55 2025

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