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Fluorine in PDB 7g2v: Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 Microm, PDB code: 7g2v was solved by M.Stihle, J.Benz, D.Hunziker, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.61 / 1.52
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.815, 91.549, 119.348, 90, 90, 90
R / Rfree (%) 18 / 21.2

Other elements in 7g2v:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 Microm also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 Microm (pdb code 7g2v). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 Microm, PDB code: 7g2v:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7g2v

Go back to Fluorine Binding Sites List in 7g2v
Fluorine binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 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 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:52.2
occ:1.00
 F33 A:XIV901 0.0 52.2 1.0
C3 A:XIV901 1.3 46.5 1.0
C4 A:XIV901 2.4 40.7 1.0
C2 A:XIV901 2.4 45.2 1.0
F34 A:XIV901 2.7 47.2 1.0
C7 A:XIV901 2.9 42.9 1.0
N9 A:XIV901 2.9 32.5 1.0
C10 A:XIV901 3.0 34.1 1.0
CD2 A:LEU243 3.2 49.8 1.0
CE2 A:PHE210 3.5 34.4 1.0
C5 A:XIV901 3.7 43.5 1.0
C1 A:XIV901 3.7 38.8 1.0
CZ A:PHE210 3.7 32.8 1.0
O8 A:XIV901 3.9 45.6 1.0
C15 A:XIV901 4.1 35.5 1.0
CD2 A:PHE210 4.1 33.3 1.0
C6 A:XIV901 4.2 36.7 1.0
C11 A:XIV901 4.5 29.1 1.0
CE1 A:PHE210 4.5 31.6 1.0
CG A:LEU243 4.5 48.2 1.0
CG A:PHE210 4.8 25.4 1.0
CG2 A:THR209 4.8 25.4 1.0
CD1 A:LEU243 4.8 51.3 1.0
CB A:THR209 4.9 24.0 1.0
CD1 A:PHE210 5.0 28.2 1.0

Fluorine binding site 2 out of 2 in 7g2v

Go back to Fluorine Binding Sites List in 7g2v
Fluorine binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 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 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:47.2
occ:1.00
 F34 A:XIV901 0.0 47.2 1.0
C2 A:XIV901 1.3 45.2 1.0
C3 A:XIV901 2.4 46.5 1.0
C1 A:XIV901 2.4 38.8 1.0
F33 A:XIV901 2.7 52.2 1.0
O37 A:XIV901 3.0 30.1 1.0
CD2 A:LEU243 3.1 49.8 1.0
S35 A:XIV901 3.2 40.2 1.0
ND2 A:ASN230 3.2 31.4 1.0
CG A:ASN230 3.5 33.1 1.0
OD1 A:ASN230 3.6 29.3 1.0
C4 A:XIV901 3.7 40.7 1.0
C6 A:XIV901 3.7 36.7 1.0
CD1 A:LEU243 3.7 51.3 1.0
N38 A:XIV901 3.8 38.8 1.0
CB A:THR209 3.8 24.0 1.0
CG A:LEU243 4.0 48.2 1.0
OG1 A:THR209 4.0 25.4 1.0
C5 A:XIV901 4.2 43.5 1.0
CD2 A:PHE210 4.4 33.3 1.0
O36 A:XIV901 4.5 34.5 1.0
CB A:ASN230 4.5 29.6 1.0
CG2 A:THR209 4.5 25.4 1.0
CE2 A:PHE210 4.7 34.4 1.0
N A:PHE210 4.8 18.4 1.0
CA A:THR209 4.8 19.5 1.0
N A:THR209 4.8 19.5 1.0
C7 A:XIV901 4.9 42.9 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: Sat Feb 8 17:51:55 2025

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