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Fluorine in PDB 7g7w: Crystal Structure of Rat Autotaxin in Complex with 4-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 Microm, PDB code: 7g7w 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) 49.23 / 1.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.725, 92.758, 120.966, 90, 90, 90
R / Rfree (%) 18.3 / 21.3

Other elements in 7g7w:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 Microm also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Calcium (Ca) 2 atoms
Chlorine (Cl) 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 4-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 Microm (pdb code 7g7w). 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 4-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 Microm, PDB code: 7g7w:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g7w

Go back to Fluorine Binding Sites List in 7g7w
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 4-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 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-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:20.6
occ:1.00
 F37 A:YAI901 0.0 20.6 1.0
C36 A:YAI901 1.3 22.6 1.0
F39 A:YAI901 2.1 24.1 1.0
F38 A:YAI901 2.2 25.4 1.0
C26 A:YAI901 2.4 20.2 1.0
C27 A:YAI901 2.7 21.6 1.0
N A:ALA217 3.3 12.1 1.0
O A:LEU213 3.3 14.0 1.0
CB A:ALA217 3.5 15.0 1.0
CA A:ALA217 3.5 13.7 1.0
CB A:LEU216 3.5 13.5 1.0
C25 A:YAI901 3.6 21.6 1.0
C A:LEU216 3.7 14.2 1.0
C28 A:YAI901 4.2 19.8 1.0
CA A:LEU216 4.2 13.2 1.0
O A:LEU216 4.3 14.3 1.0
C A:LEU213 4.4 13.6 1.0
CD1 A:LEU216 4.7 16.2 1.0
CG A:LEU216 4.8 14.3 1.0
C24 A:YAI901 4.8 20.7 1.0
CA A:LEU213 4.9 13.3 1.0
N A:LEU216 4.9 12.4 1.0
CD2 A:PHE273 4.9 20.0 1.0
CE2 A:PHE273 4.9 20.7 1.0

Fluorine binding site 2 out of 3 in 7g7w

Go back to Fluorine Binding Sites List in 7g7w
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 4-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 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-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:25.4
occ:1.00
 F38 A:YAI901 0.0 25.4 1.0
C36 A:YAI901 1.3 22.6 1.0
F39 A:YAI901 2.1 24.1 1.0
F37 A:YAI901 2.2 20.6 1.0
C26 A:YAI901 2.4 20.2 1.0
C25 A:YAI901 2.8 21.6 1.0
C27 A:YAI901 3.5 21.6 1.0
CB A:LEU216 3.6 13.5 1.0
CD1 A:LEU216 3.7 16.2 1.0
CG2 A:ILE167 4.1 16.3 1.0
C24 A:YAI901 4.2 20.7 1.0
CG A:LEU216 4.3 14.3 1.0
O A:LEU213 4.5 14.0 1.0
CD2 A:LEU213 4.6 15.9 1.0
CB A:SER169 4.6 15.8 1.0
C28 A:YAI901 4.7 19.8 1.0
CG1 A:VAL356 4.8 15.0 1.0
CA A:LEU216 4.9 13.2 1.0
C A:LEU216 4.9 14.2 1.0
OG A:SER169 4.9 18.5 1.0
CD2 A:LEU216 4.9 16.1 1.0
N A:ALA217 5.0 12.1 1.0

Fluorine binding site 3 out of 3 in 7g7w

Go back to Fluorine Binding Sites List in 7g7w
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 4-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 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 4-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:24.1
occ:1.00
 F39 A:YAI901 0.0 24.1 1.0
C36 A:YAI901 1.3 22.6 1.0
F38 A:YAI901 2.1 25.4 1.0
F37 A:YAI901 2.1 20.6 1.0
C26 A:YAI901 2.4 20.2 1.0
C25 A:YAI901 3.1 21.6 1.0
C27 A:YAI901 3.3 21.6 1.0
CD1 A:ILE167 3.7 20.4 1.0
CE2 A:PHE273 3.8 20.7 1.0
CG2 A:ILE167 3.8 16.3 1.0
CD2 A:PHE273 4.0 20.0 1.0
C24 A:YAI901 4.4 20.7 1.0
CB A:ILE167 4.4 17.0 1.0
CG1 A:ILE167 4.6 17.9 1.0
C28 A:YAI901 4.6 19.8 1.0
CB A:LEU216 4.8 13.5 1.0
CB A:ALA304 4.9 16.9 1.0
CZ A:PHE273 4.9 20.2 1.0
CE A:MET512 5.0 18.4 1.0
C23 A:YAI901 5.0 20.9 1.0
CA A:ALA217 5.0 13.7 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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