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Fluorine in PDB 7g5h: Crystal Structure of Rat Autotaxin in Complex with 1-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 1-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 Microm, PDB code: 7g5h 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) 43.39 / 2.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.712, 92.936, 121.168, 90, 90, 90
R / Rfree (%) 18.5 / 23.5

Other elements in 7g5h:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 Microm also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with 1-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 Microm (pdb code 7g5h). 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 1-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 Microm, PDB code: 7g5h:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g5h

Go back to Fluorine Binding Sites List in 7g5h
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 1-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 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-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:45.5
occ:1.00
 F34 A:YDN902 0.0 45.5 1.0
C33 A:YDN902 1.3 38.4 1.0
F35 A:YDN902 2.1 43.0 1.0
O32 A:YDN902 2.2 31.9 1.0
F36 A:YDN902 2.2 36.6 1.0
C29 A:YDN902 2.7 33.6 1.0
C28 A:YDN902 3.1 33.4 1.0
CB A:ALA217 3.3 22.2 1.0
CA A:ALA217 3.5 21.1 1.0
CE2 A:PHE273 3.6 33.2 1.0
CD2 A:PHE273 3.7 30.0 1.0
C30 A:YDN902 3.7 35.1 1.0
N A:ALA217 3.8 21.6 1.0
CZ3 A:TRP260 4.1 31.6 1.0
C27 A:YDN902 4.3 33.8 1.0
O A:LEU213 4.4 24.7 1.0
C A:LEU216 4.5 23.9 1.0
CE3 A:TRP260 4.7 30.7 1.0
CB A:LEU216 4.8 25.4 1.0
C31 A:YDN902 4.8 33.9 1.0
CD1 A:ILE167 4.9 29.1 1.0
CZ A:PHE273 4.9 31.4 1.0
O A:LEU216 4.9 21.3 1.0
C A:ALA217 5.0 21.1 1.0
CG A:PHE273 5.0 31.9 1.0

Fluorine binding site 2 out of 3 in 7g5h

Go back to Fluorine Binding Sites List in 7g5h
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 1-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 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-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:43.0
occ:1.00
 F35 A:YDN902 0.0 43.0 1.0
C33 A:YDN902 1.3 38.4 1.0
F34 A:YDN902 2.1 45.5 1.0
F36 A:YDN902 2.1 36.6 1.0
O32 A:YDN902 2.2 31.9 1.0
CB A:LEU216 3.4 25.4 1.0
C29 A:YDN902 3.4 33.6 1.0
N A:ALA217 3.8 21.6 1.0
C A:LEU216 3.8 23.9 1.0
CE A:MET512 4.1 28.6 1.0
CA A:ALA217 4.1 21.1 1.0
O A:LEU216 4.1 21.3 1.0
C30 A:YDN902 4.2 35.1 1.0
CA A:LEU216 4.3 24.1 1.0
CD1 A:LEU216 4.3 31.5 1.0
C28 A:YDN902 4.4 33.4 1.0
CG2 A:ILE167 4.4 23.0 1.0
CD1 A:ILE167 4.4 29.1 1.0
CG A:LEU216 4.4 30.5 1.0
CB A:ALA217 4.5 22.2 1.0
SD A:MET512 4.5 26.7 1.0
O A:LEU213 4.7 24.7 1.0
CE2 A:PHE273 5.0 33.2 1.0
CD2 A:LEU216 5.0 30.6 1.0

Fluorine binding site 3 out of 3 in 7g5h

Go back to Fluorine Binding Sites List in 7g5h
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 1-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 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-[(3AR,6AR)-5-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Propan-1-One, I.E. Smiles N1(C[C@H]2[C@H](C1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) CCC1CCC(CC1)Oc(F)(F)F with IC50=0.0098589 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:36.6
occ:1.00
 F36 A:YDN902 0.0 36.6 1.0
C33 A:YDN902 1.3 38.4 1.0
O32 A:YDN902 2.1 31.9 1.0
F35 A:YDN902 2.1 43.0 1.0
F34 A:YDN902 2.2 45.5 1.0
C29 A:YDN902 2.7 33.6 1.0
C30 A:YDN902 2.9 35.1 1.0
CG2 A:ILE167 3.5 23.0 1.0
CD1 A:ILE167 3.6 29.1 1.0
CE2 A:PHE273 3.6 33.2 1.0
CD2 A:PHE273 3.7 30.0 1.0
C28 A:YDN902 3.8 33.4 1.0
CB A:ILE167 4.1 22.7 1.0
C31 A:YDN902 4.1 33.9 1.0
CB A:ALA304 4.3 24.3 1.0
CG1 A:ILE167 4.4 26.2 1.0
CZ A:PHE273 4.8 31.4 1.0
C27 A:YDN902 4.8 33.8 1.0
C26 A:YDN902 4.9 34.6 1.0
CG A:PHE273 5.0 31.9 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: Tue Jul 15 20:00:04 2025

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