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Fluorine in PDB 7g7v: Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 Microm, PDB code: 7g7v 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) 48.64 / 1.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.307, 92.43, 119.114, 90, 90, 90
R / Rfree (%) 18 / 21.5

Other elements in 7g7v:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 Microm also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 Microm (pdb code 7g7v). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 Microm, PDB code: 7g7v:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7g7v

Go back to Fluorine Binding Sites List in 7g7v
Fluorine binding site 1 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 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-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:50.2
occ:1.00
 F18 A:YAW902 0.0 50.2 1.0
C9 A:YAW902 1.4 47.3 1.0
C10 A:YAW902 2.4 44.9 1.0
C8 A:YAW902 2.5 42.2 1.0
N5 A:YAW902 2.9 41.3 1.0
C4 A:YAW902 3.3 39.8 1.0
C11 A:YAW902 3.7 51.8 1.0
C13 A:YAW902 3.8 40.5 1.0
CZ A:PHE210 3.8 31.4 1.0
C3 A:YAW902 4.0 29.4 1.0
CE A:LYS248 4.1 45.1 1.0
CE1 A:PHE210 4.3 31.1 1.0
C12 A:YAW902 4.3 43.7 1.0
C6 A:YAW902 4.4 35.7 1.0
NZ A:LYS248 4.8 45.0 1.0
O A:LEU243 4.8 50.0 1.0
C7 A:YAW902 4.8 29.6 1.0

Fluorine binding site 2 out of 4 in 7g7v

Go back to Fluorine Binding Sites List in 7g7v
Fluorine binding site 2 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 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-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:22.8
occ:1.00
 F36 A:YAW902 0.0 22.8 1.0
C35 A:YAW902 1.3 24.4 1.0
F38 A:YAW902 2.1 27.0 1.0
F37 A:YAW902 2.1 25.2 1.0
C25 A:YAW902 2.3 20.0 1.0
C26 A:YAW902 2.6 20.6 1.0
O A:LEU213 3.3 17.6 1.0
N A:ALA217 3.3 15.3 1.0
CB A:LEU216 3.5 14.5 1.0
C24 A:YAW902 3.5 21.9 1.0
CA A:ALA217 3.6 16.7 1.0
CB A:ALA217 3.6 18.2 1.0
C A:LEU216 3.7 17.4 1.0
C27 A:YAW902 4.1 20.9 1.0
CA A:LEU216 4.2 15.4 1.0
C A:LEU213 4.3 15.4 1.0
O A:LEU216 4.4 16.3 1.0
C23 A:YAW902 4.7 21.9 1.0
CD1 A:LEU216 4.7 17.5 1.0
CG A:LEU216 4.8 17.1 1.0
CA A:LEU213 4.8 15.1 1.0
CD2 A:PHE273 4.8 20.0 1.0
CE2 A:PHE273 4.9 22.1 1.0
N A:LEU216 4.9 13.9 1.0
C22 A:YAW902 4.9 20.3 1.0
N30 A:YAW902 5.0 26.3 1.0

Fluorine binding site 3 out of 4 in 7g7v

Go back to Fluorine Binding Sites List in 7g7v
Fluorine binding site 3 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 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-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:25.2
occ:1.00
 F37 A:YAW902 0.0 25.2 1.0
C35 A:YAW902 1.3 24.4 1.0
F38 A:YAW902 2.0 27.0 1.0
F36 A:YAW902 2.1 22.8 1.0
C25 A:YAW902 2.4 20.0 1.0
C24 A:YAW902 2.8 21.9 1.0
C26 A:YAW902 3.5 20.6 1.0
CB A:LEU216 3.6 14.5 1.0
CD1 A:LEU216 3.7 17.5 1.0
CG2 A:ILE167 3.9 16.6 1.0
C23 A:YAW902 4.2 21.9 1.0
CG A:LEU216 4.3 17.1 1.0
CB A:SER169 4.5 19.2 1.0
CD2 A:LEU213 4.5 18.0 1.0
O A:LEU213 4.6 17.6 1.0
CG1 A:VAL356 4.7 17.5 1.0
C27 A:YAW902 4.7 20.9 1.0
CA A:LEU216 4.9 15.4 1.0
C A:LEU216 4.9 17.4 1.0
OG A:SER169 4.9 22.1 1.0
CD2 A:LEU216 4.9 17.5 1.0
N A:ALA217 5.0 15.3 1.0
C22 A:YAW902 5.0 20.3 1.0

Fluorine binding site 4 out of 4 in 7g7v

Go back to Fluorine Binding Sites List in 7g7v
Fluorine binding site 4 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 Microm


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C1C(Cc(CC1)S(=O)(=O)N)F)CCC1CCC(CC1CN1N=Nc(=N1)C) C(F)(F)F with IC50=0.0757584 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:27.0
occ:1.00
 F38 A:YAW902 0.0 27.0 1.0
C35 A:YAW902 1.3 24.4 1.0
F37 A:YAW902 2.0 25.2 1.0
F36 A:YAW902 2.1 22.8 1.0
C25 A:YAW902 2.4 20.0 1.0
C24 A:YAW902 3.0 21.9 1.0
C26 A:YAW902 3.4 20.6 1.0
CG2 A:ILE167 3.6 16.6 1.0
CE2 A:PHE273 3.7 22.1 1.0
CD1 A:ILE167 3.7 17.9 1.0
CD2 A:PHE273 3.9 20.0 1.0
CB A:ILE167 4.2 16.5 1.0
C23 A:YAW902 4.3 21.9 1.0
CG1 A:ILE167 4.5 15.5 1.0
C27 A:YAW902 4.6 20.9 1.0
CB A:LEU216 4.8 14.5 1.0
CB A:ALA304 4.9 18.7 1.0
CZ A:PHE273 4.9 21.6 1.0
CE A:MET512 4.9 16.0 1.0
C22 A:YAW902 5.0 20.3 1.0
CA A:ALA217 5.0 16.7 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 18:05:15 2025

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