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Fluorine in PDB 7g5c: Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-2-[4-(Trifluoromethoxy)Phenoxy]Ethanone, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)COC1CCC(CC1)Oc(F) (F)F with IC50=0.137048 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-2-[4-(Trifluoromethoxy)Phenoxy]Ethanone, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)COC1CCC(CC1)Oc(F) (F)F with IC50=0.137048 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-2-[4-(Trifluoromethoxy)Phenoxy]Ethanone, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)COC1CCC(CC1)Oc(F) (F)F with IC50=0.137048 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-2-[4-(Trifluoromethoxy)Phenoxy]Ethanone, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)COC1CCC(CC1)Oc(F) (F)F with IC50=0.137048 Microm, PDB code: 7g5c 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) 46.03 / 1.86
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.299, 92.055, 120.41, 90, 90, 90
R / Rfree (%) 19.2 / 23.6

Other elements in 7g5c:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-2-[4-(Trifluoromethoxy)Phenoxy]Ethanone, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)COC1CCC(CC1)Oc(F) (F)F with IC50=0.137048 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom
Potassium (K) 1 atom
Calcium (Ca) 1 atom
Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-2-[4-(Trifluoromethoxy)Phenoxy]Ethanone, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)COC1CCC(CC1)Oc(F) (F)F with IC50=0.137048 Microm (pdb code 7g5c). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-2-[4-(Trifluoromethoxy)Phenoxy]Ethanone, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)COC1CCC(CC1)Oc(F) (F)F with IC50=0.137048 Microm, PDB code: 7g5c:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7g5c

Go back to Fluorine Binding Sites List in 7g5c
Fluorine binding site 1 out of 6 in the Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-2-[4-(Trifluoromethoxy)Phenoxy]Ethanone, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)COC1CCC(CC1)Oc(F) (F)F with IC50=0.137048 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 1-[(3AS,6AS)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-2-[4-(Trifluoromethoxy)Phenoxy]Ethanone, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)COC1CCC(CC1)Oc(F) (F)F with IC50=0.137048 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:40.6
occ:0.50
 F34 A:XSK901 0.0 40.6 0.5
F34 A:ZIB902 0.0 43.2 0.5
C33 A:XSK901 1.3 41.8 0.5
C33 A:ZIB902 1.4 44.6 0.5
O32 A:XSK901 2.2 39.0 0.5
F35 A:XSK901 2.2 40.9 0.5
O32 A:ZIB902 2.2 42.6 0.5
F35 A:ZIB902 2.2 43.4 0.5
F36 A:XSK901 2.2 45.6 0.5
F36 A:ZIB902 2.3 48.2 0.5
C29 A:XSK901 3.5 36.2 0.5
C29 A:ZIB902 3.5 40.4 0.5
CB A:LEU216 3.6 20.3 1.0
C A:LEU216 3.7 20.2 1.0
N A:ALA217 3.8 18.8 1.0
O A:LEU216 3.9 20.5 1.0
CA A:ALA217 3.9 17.2 1.0
CE A:MET512 4.1 18.7 1.0
C30 A:XSK901 4.2 34.4 0.5
C30 A:ZIB902 4.2 38.9 0.5
CB A:ALA217 4.3 20.2 1.0
CA A:LEU216 4.3 18.2 1.0
CG2 A:ILE167 4.3 18.2 1.0
CD1 A:ILE167 4.5 25.9 1.0
C28 A:XSK901 4.5 34.0 0.5
C28 A:ZIB902 4.5 38.7 0.5
O A:LEU213 4.5 17.0 1.0
CE2 A:PHE273 4.6 28.6 1.0
SD A:MET512 4.7 23.7 1.0
CD1 A:LEU216 4.8 23.8 1.0
CG A:LEU216 4.8 21.9 1.0
CD2 A:PHE273 4.9 28.2 1.0

Fluorine binding site 2 out of 6 in 7g5c

Go back to Fluorine Binding Sites List in 7g5c
Fluorine binding site 2 out of 6 in the Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-2-[4-(Trifluoromethoxy)Phenoxy]Ethanone, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)COC1CCC(CC1)Oc(F) (F)F with IC50=0.137048 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 1-[(3AS,6AS)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-2-[4-(Trifluoromethoxy)Phenoxy]Ethanone, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)COC1CCC(CC1)Oc(F) (F)F with IC50=0.137048 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:40.9
occ:0.50
 F35 A:XSK901 0.0 40.9 0.5
F35 A:ZIB902 0.0 43.4 0.5
C33 A:ZIB902 1.3 44.6 0.5
C33 A:XSK901 1.3 41.8 0.5
F36 A:XSK901 2.1 45.6 0.5
F36 A:ZIB902 2.1 48.2 0.5
F34 A:ZIB902 2.1 43.2 0.5
F34 A:XSK901 2.2 40.6 0.5
O32 A:XSK901 2.2 39.0 0.5
O32 A:ZIB902 2.2 42.6 0.5
C29 A:XSK901 2.8 36.2 0.5
C29 A:ZIB902 2.8 40.4 0.5
C30 A:ZIB902 2.9 38.9 0.5
C30 A:XSK901 2.9 34.4 0.5
CD2 A:PHE273 3.3 28.2 1.0
CE2 A:PHE273 3.4 28.6 1.0
CG2 A:ILE167 3.6 18.2 1.0
CD1 A:ILE167 3.8 25.9 1.0
C28 A:XSK901 4.0 34.0 0.5
C28 A:ZIB902 4.0 38.7 0.5
CB A:ALA304 4.1 19.4 1.0
CB A:ILE167 4.2 19.6 1.0
C31 A:XSK901 4.2 32.1 0.5
C31 A:ZIB902 4.2 37.0 0.5
CG1 A:ILE167 4.6 20.5 1.0
CZ A:PHE273 4.6 28.8 1.0
CG A:PHE273 4.6 30.2 1.0
C27 A:XSK901 5.0 32.3 0.5
C27 A:ZIB902 5.0 37.3 0.5

Fluorine binding site 3 out of 6 in 7g5c

Go back to Fluorine Binding Sites List in 7g5c
Fluorine binding site 3 out of 6 in the Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-2-[4-(Trifluoromethoxy)Phenoxy]Ethanone, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)COC1CCC(CC1)Oc(F) (F)F with IC50=0.137048 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 1-[(3AS,6AS)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-2-[4-(Trifluoromethoxy)Phenoxy]Ethanone, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)COC1CCC(CC1)Oc(F) (F)F with IC50=0.137048 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:45.6
occ:0.50
 F36 A:XSK901 0.0 45.6 0.5
F36 A:ZIB902 0.0 48.2 0.5
C33 A:ZIB902 1.3 44.6 0.5
C33 A:XSK901 1.3 41.8 0.5
F35 A:ZIB902 2.1 43.4 0.5
F35 A:XSK901 2.1 40.9 0.5
O32 A:XSK901 2.2 39.0 0.5
O32 A:ZIB902 2.2 42.6 0.5
F34 A:ZIB902 2.2 43.2 0.5
F34 A:XSK901 2.2 40.6 0.5
C30 A:XSK901 2.7 34.4 0.5
C30 A:ZIB902 2.7 38.9 0.5
C29 A:XSK901 2.7 36.2 0.5
C29 A:ZIB902 2.8 40.4 0.5
CG2 A:ILE167 3.7 18.2 1.0
CB A:SER169 4.0 19.6 1.0
C31 A:XSK901 4.0 32.1 0.5
CD1 A:LEU216 4.0 23.8 1.0
C31 A:ZIB902 4.1 37.0 0.5
C28 A:XSK901 4.1 34.0 0.5
C28 A:ZIB902 4.1 38.7 0.5
CB A:LEU216 4.1 20.3 1.0
OG A:SER169 4.3 27.9 1.0
CD2 A:LEU213 4.7 15.8 1.0
CG A:LEU216 4.8 21.9 1.0
CG1 A:VAL356 4.8 17.7 1.0
CB A:ILE167 4.9 19.6 1.0
O A:LEU213 4.9 17.0 1.0

Fluorine binding site 4 out of 6 in 7g5c

Go back to Fluorine Binding Sites List in 7g5c
Fluorine binding site 4 out of 6 in the Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-2-[4-(Trifluoromethoxy)Phenoxy]Ethanone, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)COC1CCC(CC1)Oc(F) (F)F with IC50=0.137048 Microm


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-2-[4-(Trifluoromethoxy)Phenoxy]Ethanone, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)COC1CCC(CC1)Oc(F) (F)F with IC50=0.137048 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:43.2
occ:0.50
 F34 A:ZIB902 0.0 43.2 0.5
F34 A:XSK901 0.0 40.6 0.5
C33 A:XSK901 1.3 41.8 0.5
C33 A:ZIB902 1.3 44.6 0.5
O32 A:XSK901 2.1 39.0 0.5
F35 A:XSK901 2.1 40.9 0.5
O32 A:ZIB902 2.2 42.6 0.5
F35 A:ZIB902 2.2 43.4 0.5
F36 A:XSK901 2.2 45.6 0.5
F36 A:ZIB902 2.2 48.2 0.5
C29 A:XSK901 3.4 36.2 0.5
C29 A:ZIB902 3.5 40.4 0.5
CB A:LEU216 3.6 20.3 1.0
C A:LEU216 3.7 20.2 1.0
N A:ALA217 3.8 18.8 1.0
O A:LEU216 3.9 20.5 1.0
CA A:ALA217 3.9 17.2 1.0
C30 A:XSK901 4.1 34.4 0.5
C30 A:ZIB902 4.2 38.9 0.5
CE A:MET512 4.2 18.7 1.0
CB A:ALA217 4.3 20.2 1.0
CG2 A:ILE167 4.3 18.2 1.0
CA A:LEU216 4.3 18.2 1.0
CD1 A:ILE167 4.5 25.9 1.0
C28 A:XSK901 4.5 34.0 0.5
C28 A:ZIB902 4.5 38.7 0.5
O A:LEU213 4.5 17.0 1.0
CE2 A:PHE273 4.6 28.6 1.0
SD A:MET512 4.7 23.7 1.0
CD1 A:LEU216 4.8 23.8 1.0
CG A:LEU216 4.8 21.9 1.0
CD2 A:PHE273 4.9 28.2 1.0

Fluorine binding site 5 out of 6 in 7g5c

Go back to Fluorine Binding Sites List in 7g5c
Fluorine binding site 5 out of 6 in the Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-2-[4-(Trifluoromethoxy)Phenoxy]Ethanone, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)COC1CCC(CC1)Oc(F) (F)F with IC50=0.137048 Microm


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-2-[4-(Trifluoromethoxy)Phenoxy]Ethanone, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)COC1CCC(CC1)Oc(F) (F)F with IC50=0.137048 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:43.4
occ:0.50
 F35 A:ZIB902 0.0 43.4 0.5
F35 A:XSK901 0.0 40.9 0.5
C33 A:ZIB902 1.3 44.6 0.5
C33 A:XSK901 1.3 41.8 0.5
F36 A:XSK901 2.1 45.6 0.5
F36 A:ZIB902 2.1 48.2 0.5
F34 A:ZIB902 2.2 43.2 0.5
F34 A:XSK901 2.2 40.6 0.5
O32 A:ZIB902 2.2 42.6 0.5
O32 A:XSK901 2.2 39.0 0.5
C29 A:XSK901 2.8 36.2 0.5
C29 A:ZIB902 2.8 40.4 0.5
C30 A:ZIB902 2.9 38.9 0.5
C30 A:XSK901 2.9 34.4 0.5
CD2 A:PHE273 3.3 28.2 1.0
CE2 A:PHE273 3.4 28.6 1.0
CG2 A:ILE167 3.6 18.2 1.0
CD1 A:ILE167 3.8 25.9 1.0
C28 A:XSK901 3.9 34.0 0.5
C28 A:ZIB902 4.0 38.7 0.5
CB A:ALA304 4.1 19.4 1.0
CB A:ILE167 4.2 19.6 1.0
C31 A:XSK901 4.2 32.1 0.5
C31 A:ZIB902 4.2 37.0 0.5
CG1 A:ILE167 4.6 20.5 1.0
CZ A:PHE273 4.6 28.8 1.0
CG A:PHE273 4.6 30.2 1.0
C27 A:XSK901 4.9 32.3 0.5
C27 A:ZIB902 5.0 37.3 0.5

Fluorine binding site 6 out of 6 in 7g5c

Go back to Fluorine Binding Sites List in 7g5c
Fluorine binding site 6 out of 6 in the Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-2-[4-(Trifluoromethoxy)Phenoxy]Ethanone, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)COC1CCC(CC1)Oc(F) (F)F with IC50=0.137048 Microm


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-2-[4-(Trifluoromethoxy)Phenoxy]Ethanone, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)COC1CCC(CC1)Oc(F) (F)F with IC50=0.137048 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:48.2
occ:0.50
 F36 A:ZIB902 0.0 48.2 0.5
F36 A:XSK901 0.0 45.6 0.5
C33 A:ZIB902 1.3 44.6 0.5
C33 A:XSK901 1.3 41.8 0.5
F35 A:ZIB902 2.1 43.4 0.5
F35 A:XSK901 2.1 40.9 0.5
O32 A:XSK901 2.1 39.0 0.5
O32 A:ZIB902 2.2 42.6 0.5
F34 A:ZIB902 2.2 43.2 0.5
F34 A:XSK901 2.3 40.6 0.5
C30 A:XSK901 2.7 34.4 0.5
C30 A:ZIB902 2.7 38.9 0.5
C29 A:XSK901 2.7 36.2 0.5
C29 A:ZIB902 2.7 40.4 0.5
CG2 A:ILE167 3.7 18.2 1.0
CB A:SER169 4.0 19.6 1.0
C31 A:XSK901 4.0 32.1 0.5
C31 A:ZIB902 4.0 37.0 0.5
CD1 A:LEU216 4.0 23.8 1.0
C28 A:XSK901 4.1 34.0 0.5
C28 A:ZIB902 4.1 38.7 0.5
CB A:LEU216 4.1 20.3 1.0
OG A:SER169 4.2 27.9 1.0
CD2 A:LEU213 4.6 15.8 1.0
CG A:LEU216 4.8 21.9 1.0
CG1 A:VAL356 4.8 17.7 1.0
O A:LEU213 4.9 17.0 1.0
CB A:ILE167 4.9 19.6 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 17:56:12 2025

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