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Fluorine in PDB 7g6k: Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 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-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 Microm, PDB code: 7g6k 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) 49.27 / 2.29
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.689, 92.202, 121.149, 90, 90, 90
R / Rfree (%) 19.5 / 24.4

Other elements in 7g6k:

The structure of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 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 [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 Microm (pdb code 7g6k). 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-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 Microm, PDB code: 7g6k:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g6k

Go back to Fluorine Binding Sites List in 7g6k
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 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-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:65.4
occ:1.00
 F23 A:Y9L901 0.0 65.4 1.0
C22 A:Y9L901 1.3 66.3 1.0
F24 A:Y9L901 2.1 71.1 1.0
F25 A:Y9L901 2.2 63.1 1.0
O21 A:Y9L901 2.3 62.3 1.0
C18 A:Y9L901 3.4 61.8 1.0
C17 A:Y9L901 3.6 60.3 1.0
CG2 A:ILE167 3.6 28.9 1.0
CB A:LEU216 3.6 26.9 1.0
CD1 A:LEU216 3.9 31.9 1.0
CG A:LEU216 4.3 29.7 1.0
C19 A:Y9L901 4.6 60.9 1.0
C A:LEU216 4.6 26.7 1.0
CG1 A:VAL356 4.7 25.7 1.0
CB A:ILE167 4.7 29.8 1.0
CA A:LEU216 4.8 26.3 1.0
CD1 A:ILE167 4.8 29.4 1.0
N A:ALA217 4.8 26.9 1.0
O A:LEU213 4.9 29.5 1.0
CE A:MET512 4.9 30.0 1.0
CB A:SER169 4.9 31.1 1.0
O A:LEU216 4.9 27.3 1.0
C16 A:Y9L901 5.0 63.0 1.0
CD2 A:LEU216 5.0 28.9 1.0

Fluorine binding site 2 out of 3 in 7g6k

Go back to Fluorine Binding Sites List in 7g6k
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 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-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:71.1
occ:1.00
 F24 A:Y9L901 0.0 71.1 1.0
C22 A:Y9L901 1.3 66.3 1.0
F23 A:Y9L901 2.1 65.4 1.0
F25 A:Y9L901 2.2 63.1 1.0
O21 A:Y9L901 2.3 62.3 1.0
C18 A:Y9L901 2.7 61.8 1.0
C17 A:Y9L901 2.7 60.3 1.0
CE2 A:PHE273 3.5 42.2 1.0
CD2 A:PHE273 3.6 41.0 1.0
CG2 A:ILE167 3.6 28.9 1.0
C19 A:Y9L901 3.9 60.9 1.0
C16 A:Y9L901 3.9 63.0 1.0
CD1 A:ILE167 4.0 29.4 1.0
CB A:ILE167 4.1 29.8 1.0
CB A:ALA304 4.4 31.6 1.0
CG1 A:ILE167 4.6 28.2 1.0
CZ A:PHE273 4.8 39.2 1.0
C20 A:Y9L901 4.8 62.9 1.0
CG A:PHE273 4.8 41.8 1.0
C15 A:Y9L901 4.8 63.4 1.0

Fluorine binding site 3 out of 3 in 7g6k

Go back to Fluorine Binding Sites List in 7g6k
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 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-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:63.1
occ:1.00
 F25 A:Y9L901 0.0 63.1 1.0
C22 A:Y9L901 1.4 66.3 1.0
F24 A:Y9L901 2.2 71.1 1.0
F23 A:Y9L901 2.2 65.4 1.0
O21 A:Y9L901 2.3 62.3 1.0
C18 A:Y9L901 3.5 61.8 1.0
CA A:ALA217 3.6 26.5 1.0
CB A:ALA217 3.7 26.0 1.0
N A:ALA217 3.7 26.9 1.0
C A:LEU216 3.9 26.7 1.0
CE2 A:PHE273 4.0 42.2 1.0
O A:LEU216 4.1 27.3 1.0
CB A:LEU216 4.2 26.9 1.0
C17 A:Y9L901 4.2 60.3 1.0
CE A:MET512 4.3 30.0 1.0
C19 A:Y9L901 4.4 60.9 1.0
CD2 A:PHE273 4.4 41.0 1.0
CD1 A:ILE167 4.6 29.4 1.0
O A:LEU213 4.6 29.5 1.0
CA A:LEU216 4.7 26.3 1.0
CG2 A:ILE167 4.9 28.9 1.0
SD A:MET512 4.9 31.6 1.0
C A:ALA217 4.9 27.4 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: Tue Jul 15 20:03:43 2025

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