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Fluorine in PDB 7g4u: Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AS,8AR)-2- [(5R)-4,5,6,7-Tetrahydro-1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,5,7,8, 8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.0213266 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AS,8AR)-2- [(5R)-4,5,6,7-Tetrahydro-1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,5,7,8, 8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.0213266 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AS,8AR)-2- [(5R)-4,5,6,7-Tetrahydro-1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,5,7,8, 8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.0213266 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AS,8AR)-2- [(5R)-4,5,6,7-Tetrahydro-1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,5,7,8, 8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.0213266 Microm, PDB code: 7g4u 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) 46.32 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.353, 92.64, 120.027, 90, 90, 90
R / Rfree (%) 19.3 / 23.4

Other elements in 7g4u:

The structure of Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AS,8AR)-2- [(5R)-4,5,6,7-Tetrahydro-1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,5,7,8, 8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.0213266 Microm also contains other interesting chemical elements:

Zinc (Zn) 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 (E)-1-[(3AS,8AR)-2- [(5R)-4,5,6,7-Tetrahydro-1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,5,7,8, 8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.0213266 Microm (pdb code 7g4u). 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 (E)-1-[(3AS,8AR)-2- [(5R)-4,5,6,7-Tetrahydro-1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,5,7,8, 8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.0213266 Microm, PDB code: 7g4u:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g4u

Go back to Fluorine Binding Sites List in 7g4u
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AS,8AR)-2- [(5R)-4,5,6,7-Tetrahydro-1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,5,7,8, 8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.0213266 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 (E)-1-[(3AS,8AR)-2- [(5R)-4,5,6,7-Tetrahydro-1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,5,7,8, 8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.0213266 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:29.9
occ:1.00
 F25 A:X82901 0.0 29.9 1.0
C24 A:X82901 1.3 33.0 1.0
F27 A:X82901 2.2 37.3 1.0
F26 A:X82901 2.2 33.4 1.0
O23 A:X82901 2.2 31.8 1.0
C A:LEU216 3.5 16.6 1.0
C20 A:X82901 3.5 31.4 1.0
CE A:MET512 3.5 18.8 1.0
O A:LEU216 3.6 14.7 1.0
CB A:LEU216 3.6 17.0 1.0
N A:ALA217 3.6 15.1 1.0
CA A:ALA217 3.7 14.7 1.0
SD A:MET512 4.1 18.7 1.0
CA A:LEU216 4.2 15.6 1.0
C19 A:X82901 4.3 27.0 1.0
CD1 A:ILE167 4.4 20.7 1.0
CB A:ALA217 4.4 16.1 1.0
C21 A:X82901 4.5 29.9 1.0
CG2 A:ILE167 4.6 16.8 1.0
CG A:LEU216 4.9 17.4 1.0
O A:LEU213 4.9 14.8 1.0

Fluorine binding site 2 out of 3 in 7g4u

Go back to Fluorine Binding Sites List in 7g4u
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AS,8AR)-2- [(5R)-4,5,6,7-Tetrahydro-1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,5,7,8, 8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.0213266 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 (E)-1-[(3AS,8AR)-2- [(5R)-4,5,6,7-Tetrahydro-1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,5,7,8, 8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.0213266 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:33.4
occ:1.00
 F26 A:X82901 0.0 33.4 1.0
C24 A:X82901 1.3 33.0 1.0
F27 A:X82901 2.1 37.3 1.0
O23 A:X82901 2.2 31.8 1.0
F25 A:X82901 2.2 29.9 1.0
C20 A:X82901 2.7 31.4 1.0
CB A:ALA217 3.3 16.1 1.0
C21 A:X82901 3.3 29.9 1.0
CA A:ALA217 3.5 14.7 1.0
C19 A:X82901 3.5 27.0 1.0
N A:ALA217 3.8 15.1 1.0
CD2 A:PHE273 3.9 24.8 1.0
CZ3 A:TRP260 3.9 22.3 1.0
CE2 A:PHE273 4.0 23.3 1.0
O A:LEU213 4.4 14.8 1.0
C A:LEU216 4.4 16.6 1.0
C22 A:X82901 4.4 27.9 1.0
CE3 A:TRP260 4.5 22.1 1.0
C18 A:X82901 4.6 27.1 1.0
O A:LEU216 4.8 14.7 1.0
CB A:LEU216 4.8 17.0 1.0
C A:ALA217 4.9 15.8 1.0
C17 A:X82901 5.0 25.3 1.0
CH2 A:TRP260 5.0 22.2 1.0

Fluorine binding site 3 out of 3 in 7g4u

Go back to Fluorine Binding Sites List in 7g4u
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AS,8AR)-2- [(5R)-4,5,6,7-Tetrahydro-1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,5,7,8, 8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.0213266 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 (E)-1-[(3AS,8AR)-2- [(5R)-4,5,6,7-Tetrahydro-1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,5,7,8, 8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4-(Trifluoromethoxy) Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.0213266 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:37.3
occ:1.00
 F27 A:X82901 0.0 37.3 1.0
C24 A:X82901 1.3 33.0 1.0
F26 A:X82901 2.1 33.4 1.0
O23 A:X82901 2.2 31.8 1.0
F25 A:X82901 2.2 29.9 1.0
C20 A:X82901 2.8 31.4 1.0
C19 A:X82901 2.8 27.0 1.0
CD1 A:ILE167 3.2 20.7 1.0
CE2 A:PHE273 3.6 23.3 1.0
CG2 A:ILE167 3.6 16.8 1.0
CD2 A:PHE273 3.7 24.8 1.0
CB A:ILE167 4.0 17.9 1.0
CG1 A:ILE167 4.0 18.9 1.0
C21 A:X82901 4.0 29.9 1.0
C18 A:X82901 4.1 27.1 1.0
CB A:ALA304 4.5 16.8 1.0
CZ A:PHE273 4.7 22.8 1.0
SD A:MET512 4.8 18.7 1.0
CG A:PHE273 4.9 24.5 1.0
CE A:MET512 4.9 18.8 1.0
CD2 A:LEU259 5.0 16.7 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 17:54:05 2025

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