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Fluorine in PDB 5s9n: Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3%

Enzymatic activity of Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3%

All present enzymatic activity of Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3%:
3.1.4.39;

Protein crystallography data

The structure of Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3%, PDB code: 5s9n was solved by M.Stihle, D.Hunziker, J.Benz, P.Mattei, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.90 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.114, 91.731, 120.21, 90, 90, 90
R / Rfree (%) 19.1 / 23.3

Other elements in 5s9n:

The structure of Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3% also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Zinc (Zn) 1 atom
Calcium (Ca) 2 atoms
Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3% (pdb code 5s9n). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3%, PDB code: 5s9n:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5s9n

Go back to Fluorine Binding Sites List in 5s9n
Fluorine binding site 1 out of 3 in the Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3%


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:55.2
occ:1.00
 F34 A:YVS901 0.0 55.2 1.0
C33 A:YVS901 1.4 51.0 1.0
F35 A:YVS901 2.2 47.0 1.0
F36 A:YVS901 2.2 53.8 1.0
O32 A:YVS901 2.4 43.0 1.0
C29 A:YVS901 2.9 50.1 1.0
C30 A:YVS901 3.1 45.1 1.0
CB A:ALA217 3.2 20.1 1.0
CD2 A:PHE273 3.4 30.9 1.0
CA A:ALA217 3.5 18.4 1.0
CE2 A:PHE273 3.5 30.9 1.0
CZ3 A:TRP260 3.8 27.8 1.0
N A:ALA217 3.8 17.8 1.0
C28 A:YVS901 4.0 47.0 1.0
C31 A:YVS901 4.2 51.9 1.0
CE3 A:TRP260 4.4 27.4 1.0
O A:LEU213 4.5 17.1 1.0
C A:LEU216 4.5 21.1 1.0
CG A:PHE273 4.8 34.0 1.0
C A:ALA217 4.8 18.0 1.0
O A:LEU216 4.8 21.2 1.0
CH2 A:TRP260 4.9 29.9 1.0
CZ A:PHE273 4.9 32.0 1.0
CB A:LEU216 4.9 19.3 1.0
C27 A:YVS901 5.0 49.5 1.0

Fluorine binding site 2 out of 3 in 5s9n

Go back to Fluorine Binding Sites List in 5s9n
Fluorine binding site 2 out of 3 in the Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3%


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:47.0
occ:1.00
 F35 A:YVS901 0.0 47.0 1.0
C33 A:YVS901 1.3 51.0 1.0
F34 A:YVS901 2.2 55.2 1.0
F36 A:YVS901 2.2 53.8 1.0
O32 A:YVS901 2.2 43.0 1.0
CB A:LEU216 3.4 19.3 1.0
C29 A:YVS901 3.5 50.1 1.0
C A:LEU216 3.5 21.1 1.0
N A:ALA217 3.6 17.8 1.0
O A:LEU216 3.8 21.2 1.0
CA A:ALA217 3.8 18.4 1.0
CE A:MET512 3.9 22.1 1.0
CA A:LEU216 4.1 20.3 1.0
C30 A:YVS901 4.2 45.1 1.0
CB A:ALA217 4.3 20.1 1.0
SD A:MET512 4.4 25.2 1.0
C28 A:YVS901 4.4 47.0 1.0
CG2 A:ILE167 4.5 21.6 1.0
O A:LEU213 4.5 17.1 1.0
CD1 A:ILE167 4.7 31.0 1.0
CG A:LEU216 4.7 23.3 1.0
CD1 A:LEU216 4.9 25.4 1.0
CE2 A:PHE273 4.9 30.9 1.0

Fluorine binding site 3 out of 3 in 5s9n

Go back to Fluorine Binding Sites List in 5s9n
Fluorine binding site 3 out of 3 in the Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3%


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:53.8
occ:1.00
 F36 A:YVS901 0.0 53.8 1.0
C33 A:YVS901 1.3 51.0 1.0
F35 A:YVS901 2.2 47.0 1.0
O32 A:YVS901 2.2 43.0 1.0
F34 A:YVS901 2.2 55.2 1.0
C29 A:YVS901 2.8 50.1 1.0
C28 A:YVS901 3.2 47.0 1.0
CE2 A:PHE273 3.4 30.9 1.0
CD1 A:ILE167 3.5 31.0 1.0
CG2 A:ILE167 3.5 21.6 1.0
CD2 A:PHE273 3.6 30.9 1.0
C30 A:YVS901 3.8 45.1 1.0
CB A:ILE167 4.0 20.3 1.0
CG1 A:ILE167 4.3 24.6 1.0
CB A:ALA304 4.3 23.6 1.0
C27 A:YVS901 4.4 49.5 1.0
CZ A:PHE273 4.7 32.0 1.0
C31 A:YVS901 4.8 51.9 1.0
CG A:PHE273 4.9 34.0 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: Tue Jul 15 07:05:57 2025

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