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Fluorine in PDB 7g7b: Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-3A-Methyl-2-(4- Sulfamoylbenzoyl)-3,4,6,6A-Tetrahydro-1H-Pyrrolo[3,4-C]Pyrrole-5- Carboxylate, I.E. Smiles Ns(=O)(=O)C1CCC(CC1)C(=O)N1C[C@]2(Cn(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@@H]2C1)C with IC50=0.0121906 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-3A-Methyl-2-(4- Sulfamoylbenzoyl)-3,4,6,6A-Tetrahydro-1H-Pyrrolo[3,4-C]Pyrrole-5- Carboxylate, I.E. Smiles Ns(=O)(=O)C1CCC(CC1)C(=O)N1C[C@]2(Cn(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@@H]2C1)C with IC50=0.0121906 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-3A-Methyl-2-(4- Sulfamoylbenzoyl)-3,4,6,6A-Tetrahydro-1H-Pyrrolo[3,4-C]Pyrrole-5- Carboxylate, I.E. Smiles Ns(=O)(=O)C1CCC(CC1)C(=O)N1C[C@]2(Cn(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@@H]2C1)C with IC50=0.0121906 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-3A-Methyl-2-(4- Sulfamoylbenzoyl)-3,4,6,6A-Tetrahydro-1H-Pyrrolo[3,4-C]Pyrrole-5- Carboxylate, I.E. Smiles Ns(=O)(=O)C1CCC(CC1)C(=O)N1C[C@]2(Cn(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@@H]2C1)C with IC50=0.0121906 Microm, PDB code: 7g7b 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) 48.77 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.901, 91.47, 119.86, 90, 90, 90
R / Rfree (%) 19 / 23

Other elements in 7g7b:

The structure of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-3A-Methyl-2-(4- Sulfamoylbenzoyl)-3,4,6,6A-Tetrahydro-1H-Pyrrolo[3,4-C]Pyrrole-5- Carboxylate, I.E. Smiles Ns(=O)(=O)C1CCC(CC1)C(=O)N1C[C@]2(Cn(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@@H]2C1)C with IC50=0.0121906 Microm also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Sodium (Na) 1 atom
Zinc (Zn) 1 atom
Chlorine (Cl) 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 [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-3A-Methyl-2-(4- Sulfamoylbenzoyl)-3,4,6,6A-Tetrahydro-1H-Pyrrolo[3,4-C]Pyrrole-5- Carboxylate, I.E. Smiles Ns(=O)(=O)C1CCC(CC1)C(=O)N1C[C@]2(Cn(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@@H]2C1)C with IC50=0.0121906 Microm (pdb code 7g7b). 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- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-3A-Methyl-2-(4- Sulfamoylbenzoyl)-3,4,6,6A-Tetrahydro-1H-Pyrrolo[3,4-C]Pyrrole-5- Carboxylate, I.E. Smiles Ns(=O)(=O)C1CCC(CC1)C(=O)N1C[C@]2(Cn(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@@H]2C1)C with IC50=0.0121906 Microm, PDB code: 7g7b:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g7b

Go back to Fluorine Binding Sites List in 7g7b
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-3A-Methyl-2-(4- Sulfamoylbenzoyl)-3,4,6,6A-Tetrahydro-1H-Pyrrolo[3,4-C]Pyrrole-5- Carboxylate, I.E. Smiles Ns(=O)(=O)C1CCC(CC1)C(=O)N1C[C@]2(Cn(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@@H]2C1)C with IC50=0.0121906 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- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-3A-Methyl-2-(4- Sulfamoylbenzoyl)-3,4,6,6A-Tetrahydro-1H-Pyrrolo[3,4-C]Pyrrole-5- Carboxylate, I.E. Smiles Ns(=O)(=O)C1CCC(CC1)C(=O)N1C[C@]2(Cn(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@@H]2C1)C with IC50=0.0121906 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:44.4
occ:1.00
 F27 A:XUT901 0.0 44.4 1.0
C26 A:XUT901 1.3 45.3 1.0
F28 A:XUT901 2.1 39.0 1.0
F29 A:XUT901 2.2 53.0 1.0
O25 A:XUT901 2.3 40.4 1.0
C24 A:XUT901 2.9 40.5 1.0
C23 A:XUT901 2.9 39.7 1.0
CE2 A:PHE273 3.4 33.9 1.0
CD1 A:ILE167 3.5 27.2 1.0
CG2 A:ILE167 3.7 21.6 1.0
CD2 A:PHE273 3.7 31.4 1.0
CB A:ILE167 4.0 23.2 1.0
C30 A:XUT901 4.0 39.7 1.0
C22 A:XUT901 4.1 40.0 1.0
CG1 A:ILE167 4.2 24.9 1.0
CZ A:PHE273 4.6 31.3 1.0
CB A:ALA304 4.6 23.2 1.0
SD A:MET512 4.9 25.0 1.0
C31 A:XUT901 5.0 41.3 1.0
C21 A:XUT901 5.0 43.3 1.0

Fluorine binding site 2 out of 3 in 7g7b

Go back to Fluorine Binding Sites List in 7g7b
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-3A-Methyl-2-(4- Sulfamoylbenzoyl)-3,4,6,6A-Tetrahydro-1H-Pyrrolo[3,4-C]Pyrrole-5- Carboxylate, I.E. Smiles Ns(=O)(=O)C1CCC(CC1)C(=O)N1C[C@]2(Cn(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@@H]2C1)C with IC50=0.0121906 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- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-3A-Methyl-2-(4- Sulfamoylbenzoyl)-3,4,6,6A-Tetrahydro-1H-Pyrrolo[3,4-C]Pyrrole-5- Carboxylate, I.E. Smiles Ns(=O)(=O)C1CCC(CC1)C(=O)N1C[C@]2(Cn(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@@H]2C1)C with IC50=0.0121906 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:39.0
occ:1.00
 F28 A:XUT901 0.0 39.0 1.0
C26 A:XUT901 1.3 45.3 1.0
F27 A:XUT901 2.1 44.4 1.0
O25 A:XUT901 2.2 40.4 1.0
F29 A:XUT901 2.2 53.0 1.0
N A:ALA217 3.4 19.5 1.0
CA A:ALA217 3.4 19.3 1.0
C A:LEU216 3.5 19.8 1.0
C24 A:XUT901 3.5 40.5 1.0
O A:LEU216 3.6 19.6 1.0
CB A:LEU216 3.6 21.1 1.0
CE A:MET512 3.8 22.7 1.0
CB A:ALA217 3.9 19.8 1.0
C23 A:XUT901 4.1 39.7 1.0
CA A:LEU216 4.2 19.6 1.0
SD A:MET512 4.5 25.0 1.0
C30 A:XUT901 4.5 39.7 1.0
O A:LEU213 4.5 20.4 1.0
CE2 A:PHE273 4.6 33.9 1.0
CD1 A:ILE167 4.6 27.2 1.0
C A:ALA217 4.8 19.4 1.0
CG2 A:ILE167 4.9 21.6 1.0
CG A:LEU216 4.9 24.5 1.0

Fluorine binding site 3 out of 3 in 7g7b

Go back to Fluorine Binding Sites List in 7g7b
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-3A-Methyl-2-(4- Sulfamoylbenzoyl)-3,4,6,6A-Tetrahydro-1H-Pyrrolo[3,4-C]Pyrrole-5- Carboxylate, I.E. Smiles Ns(=O)(=O)C1CCC(CC1)C(=O)N1C[C@]2(Cn(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@@H]2C1)C with IC50=0.0121906 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- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-3A-Methyl-2-(4- Sulfamoylbenzoyl)-3,4,6,6A-Tetrahydro-1H-Pyrrolo[3,4-C]Pyrrole-5- Carboxylate, I.E. Smiles Ns(=O)(=O)C1CCC(CC1)C(=O)N1C[C@]2(Cn(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@@H]2C1)C with IC50=0.0121906 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:53.0
occ:1.00
 F29 A:XUT901 0.0 53.0 1.0
C26 A:XUT901 1.4 45.3 1.0
F27 A:XUT901 2.2 44.4 1.0
F28 A:XUT901 2.2 39.0 1.0
O25 A:XUT901 2.2 40.4 1.0
C23 A:XUT901 3.0 39.7 1.0
C24 A:XUT901 3.1 40.5 1.0
CG2 A:ILE167 3.5 21.6 1.0
CB A:LEU216 3.6 21.1 1.0
CD1 A:LEU216 3.8 30.2 1.0
CG A:LEU216 4.3 24.5 1.0
C22 A:XUT901 4.4 40.0 1.0
C30 A:XUT901 4.4 39.7 1.0
CG1 A:VAL356 4.6 20.0 1.0
CB A:ILE167 4.6 23.2 1.0
CB A:SER169 4.7 29.3 1.0
C A:LEU216 4.8 19.8 1.0
CD2 A:LEU216 4.8 26.1 1.0
CA A:LEU216 4.8 19.6 1.0
CD1 A:ILE167 4.8 27.2 1.0
N A:ALA217 4.9 19.5 1.0
O A:LEU213 5.0 20.4 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 18:05:16 2025

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