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Fluorine in PDB 7g7e: Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AR,6AR)-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@@H]2CN(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@]2(C1)C with IC50=0.0156721 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AR,6AR)-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@@H]2CN(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@]2(C1)C with IC50=0.0156721 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AR,6AR)-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@@H]2CN(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@]2(C1)C with IC50=0.0156721 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AR,6AR)-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@@H]2CN(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@]2(C1)C with IC50=0.0156721 Microm, PDB code: 7g7e 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) 43.00 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.962, 91.337, 119.725, 90, 90, 90
R / Rfree (%) 19.3 / 24.1

Other elements in 7g7e:

The structure of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AR,6AR)-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@@H]2CN(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@]2(C1)C with IC50=0.0156721 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 (3AR,6AR)-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@@H]2CN(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@]2(C1)C with IC50=0.0156721 Microm (pdb code 7g7e). 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 (3AR,6AR)-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@@H]2CN(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@]2(C1)C with IC50=0.0156721 Microm, PDB code: 7g7e:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g7e

Go back to Fluorine Binding Sites List in 7g7e
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AR,6AR)-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@@H]2CN(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@]2(C1)C with IC50=0.0156721 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 (3AR,6AR)-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@@H]2CN(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@]2(C1)C with IC50=0.0156721 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:56.3
occ:1.00
 F27 A:Y8K901 0.0 56.3 1.0
C26 A:Y8K901 1.4 52.2 1.0
F28 A:Y8K901 2.1 55.5 1.0
F29 A:Y8K901 2.2 58.8 1.0
O25 A:Y8K901 2.3 46.3 1.0
C24 A:Y8K901 3.0 44.4 1.0
CE2 A:PHE273 3.3 33.3 1.0
CB A:ALA217 3.3 19.2 1.0
C30 A:Y8K901 3.4 43.8 1.0
CD2 A:PHE273 3.5 32.3 1.0
CA A:ALA217 3.5 19.1 1.0
CZ3 A:TRP260 3.8 22.5 1.0
C23 A:Y8K901 3.9 40.6 1.0
N A:ALA217 3.9 18.8 1.0
CE3 A:TRP260 4.4 23.9 1.0
CZ A:PHE273 4.5 30.4 1.0
C A:LEU216 4.5 21.1 1.0
C31 A:Y8K901 4.6 44.6 1.0
O A:LEU213 4.7 19.8 1.0
C A:ALA217 4.8 19.4 1.0
O A:LEU216 4.8 19.9 1.0
CG A:PHE273 4.8 33.2 1.0
CB A:LEU259 4.9 21.4 1.0
CB A:LEU216 4.9 22.7 1.0
CH2 A:TRP260 5.0 24.4 1.0
CD1 A:ILE167 5.0 24.2 1.0
C22 A:Y8K901 5.0 42.4 1.0

Fluorine binding site 2 out of 3 in 7g7e

Go back to Fluorine Binding Sites List in 7g7e
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AR,6AR)-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@@H]2CN(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@]2(C1)C with IC50=0.0156721 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 (3AR,6AR)-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@@H]2CN(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@]2(C1)C with IC50=0.0156721 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:55.5
occ:1.00
 F28 A:Y8K901 0.0 55.5 1.0
C26 A:Y8K901 1.3 52.2 1.0
F29 A:Y8K901 2.1 58.8 1.0
F27 A:Y8K901 2.1 56.3 1.0
O25 A:Y8K901 2.2 46.3 1.0
CB A:LEU216 3.2 22.7 1.0
C A:LEU216 3.4 21.1 1.0
N A:ALA217 3.4 18.8 1.0
C24 A:Y8K901 3.5 44.4 1.0
O A:LEU216 3.7 19.9 1.0
CA A:ALA217 3.7 19.1 1.0
CE A:MET512 3.8 23.0 1.0
CA A:LEU216 3.9 21.2 1.0
CB A:ALA217 4.1 19.2 1.0
C23 A:Y8K901 4.2 40.6 1.0
O A:LEU213 4.4 19.8 1.0
CG A:LEU216 4.4 28.6 1.0
SD A:MET512 4.5 24.2 1.0
C30 A:Y8K901 4.5 43.8 1.0
CG2 A:ILE167 4.6 20.8 1.0
CD1 A:LEU216 4.7 33.5 1.0
CD1 A:ILE167 4.9 24.2 1.0
CE2 A:PHE273 4.9 33.3 1.0
CD2 A:LEU216 4.9 29.7 1.0

Fluorine binding site 3 out of 3 in 7g7e

Go back to Fluorine Binding Sites List in 7g7e
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AR,6AR)-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@@H]2CN(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@]2(C1)C with IC50=0.0156721 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 (3AR,6AR)-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@@H]2CN(C(=O) OCC3CCC(Oc(F)(F)F)CC3)C[C@]2(C1)C with IC50=0.0156721 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:58.8
occ:1.00
 F29 A:Y8K901 0.0 58.8 1.0
C26 A:Y8K901 1.3 52.2 1.0
F28 A:Y8K901 2.1 55.5 1.0
O25 A:Y8K901 2.2 46.3 1.0
F27 A:Y8K901 2.2 56.3 1.0
C24 A:Y8K901 2.8 44.4 1.0
C23 A:Y8K901 3.0 40.6 1.0
CG2 A:ILE167 3.4 20.8 1.0
CE2 A:PHE273 3.6 33.3 1.0
CD1 A:ILE167 3.6 24.2 1.0
CB A:ILE167 3.8 21.4 1.0
CD2 A:PHE273 4.0 32.3 1.0
C30 A:Y8K901 4.0 43.8 1.0
CG1 A:ILE167 4.1 21.7 1.0
C22 A:Y8K901 4.1 42.4 1.0
CB A:ALA304 4.7 22.0 1.0
CZ A:PHE273 4.7 30.4 1.0
SD A:MET512 4.9 24.2 1.0
C31 A:Y8K901 5.0 44.6 1.0
CE A:MET512 5.0 23.0 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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