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Fluorine in PDB 7g4n: Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 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)-2-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 Microm, PDB code: 7g4n 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) 45.74 / 1.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.726, 91.477, 118.973, 90, 90, 90
R / Rfree (%) 18 / 21.5

Other elements in 7g4n:

The structure of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom
Sodium (Na) 2 atoms
Calcium (Ca) 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)-2-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 Microm (pdb code 7g4n). 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)-2-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 Microm, PDB code: 7g4n:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g4n

Go back to Fluorine Binding Sites List in 7g4n
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 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)-2-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:31.2
occ:1.00
 F1 A:Y9S901 0.0 31.2 1.0
C2 A:Y9S901 1.3 35.9 1.0
F4 A:Y9S901 2.2 35.6 1.0
F5 A:Y9S901 2.2 32.7 1.0
O3 A:Y9S901 2.2 31.4 1.0
C A:LEU216 3.4 14.8 1.0
CB A:LEU216 3.5 14.5 1.0
N A:ALA217 3.5 13.4 1.0
C6 A:Y9S901 3.5 29.2 1.0
O A:LEU216 3.6 16.0 1.0
CA A:ALA217 3.6 14.2 1.0
CE A:MET512 3.7 16.9 1.0
CA A:LEU216 4.1 13.6 1.0
CB A:ALA217 4.1 15.4 1.0
SD A:MET512 4.3 19.1 1.0
C7 A:Y9S901 4.3 27.3 1.0
C11 A:Y9S901 4.5 31.3 1.0
O A:LEU213 4.5 14.6 1.0
CD1 A:ILE167 4.7 21.3 1.0
CG A:LEU216 4.7 17.3 1.0
CG2 A:ILE167 4.8 19.2 1.0
CE2 A:PHE273 4.8 25.8 1.0
C A:ALA217 4.9 14.1 1.0
CD1 A:LEU216 4.9 22.1 1.0

Fluorine binding site 2 out of 3 in 7g4n

Go back to Fluorine Binding Sites List in 7g4n
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 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)-2-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:35.6
occ:1.00
 F4 A:Y9S901 0.0 35.6 1.0
C2 A:Y9S901 1.3 35.9 1.0
F1 A:Y9S901 2.2 31.2 1.0
F5 A:Y9S901 2.2 32.7 1.0
O3 A:Y9S901 2.3 31.4 1.0
C6 A:Y9S901 2.9 29.2 1.0
C11 A:Y9S901 3.2 31.3 1.0
CE2 A:PHE273 3.3 25.8 1.0
CD2 A:PHE273 3.3 23.7 1.0
CB A:ALA217 3.4 15.4 1.0
CA A:ALA217 3.6 14.2 1.0
CZ3 A:TRP260 3.8 18.3 1.0
C7 A:Y9S901 3.9 27.3 1.0
N A:ALA217 4.1 13.4 1.0
CE3 A:TRP260 4.3 20.3 1.0
C10 A:Y9S901 4.5 29.7 1.0
CZ A:PHE273 4.6 27.2 1.0
O A:LEU213 4.6 14.6 1.0
CG A:PHE273 4.6 24.6 1.0
C A:LEU216 4.7 14.8 1.0
CB A:LEU259 4.9 16.1 1.0
C A:ALA217 4.9 14.1 1.0
C8 A:Y9S901 4.9 30.2 1.0
CH2 A:TRP260 5.0 16.4 1.0
O A:LEU216 5.0 16.0 1.0

Fluorine binding site 3 out of 3 in 7g4n

Go back to Fluorine Binding Sites List in 7g4n
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 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)-2-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:32.7
occ:1.00
 F5 A:Y9S901 0.0 32.7 1.0
C2 A:Y9S901 1.4 35.9 1.0
F1 A:Y9S901 2.2 31.2 1.0
F4 A:Y9S901 2.2 35.6 1.0
O3 A:Y9S901 2.3 31.4 1.0
C6 A:Y9S901 2.8 29.2 1.0
C7 A:Y9S901 3.0 27.3 1.0
CE2 A:PHE273 3.4 25.8 1.0
CD1 A:ILE167 3.5 21.3 1.0
CG2 A:ILE167 3.5 19.2 1.0
CD2 A:PHE273 3.7 23.7 1.0
CB A:ILE167 3.8 18.0 1.0
C11 A:Y9S901 3.9 31.3 1.0
CG1 A:ILE167 4.1 18.7 1.0
C8 A:Y9S901 4.2 30.2 1.0
CB A:ALA304 4.5 15.0 1.0
CZ A:PHE273 4.6 27.2 1.0
SD A:MET512 4.8 19.1 1.0
C10 A:Y9S901 4.9 29.7 1.0
CE A:MET512 5.0 16.9 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 17:51:54 2025

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