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Fluorine in PDB 7g7j: Crystal Structure of Rat Autotaxin in Complex with 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 Microm, PDB code: 7g7j 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) 45.83 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.045, 91.656, 118.945, 90, 90, 90
R / Rfree (%) 18.6 / 22.8

Other elements in 7g7j:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 Microm also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 Microm (pdb code 7g7j). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Rat Autotaxin in Complex with 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 Microm, PDB code: 7g7j:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7g7j

Go back to Fluorine Binding Sites List in 7g7j
Fluorine binding site 1 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 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-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:53.2
occ:1.00
 F17 A:XSB901 0.0 53.2 1.0
C8 A:XSB901 1.4 48.6 1.0
C7 A:XSB901 2.5 44.6 1.0
C9 A:XSB901 2.5 45.6 1.0
C5 A:XSB901 2.9 42.1 1.0
OH A:TYR306 2.9 28.9 1.0
N4 A:XSB901 3.2 34.4 1.0
OD2 A:ASP171 3.5 41.2 1.0
O A:HOH1182 3.5 36.8 1.0
C18 A:XSB901 3.6 33.9 1.0
O6 A:XSB901 3.7 46.6 1.0
C12 A:XSB901 3.8 52.7 1.0
C10 A:XSB901 3.8 51.4 1.0
CZ A:TYR306 4.0 24.3 1.0
C3 A:XSB901 4.2 32.8 1.0
CE2 A:TYR306 4.3 25.9 1.0
C11 A:XSB901 4.3 49.0 1.0
C2 A:XSB901 4.4 31.6 1.0
CG A:GLU308 4.4 44.3 1.0
CB A:GLU308 4.6 33.9 1.0
CG A:ASP171 4.6 31.4 1.0
CA A:GLU308 4.7 28.2 1.0
C19 A:XSB901 4.7 31.1 1.0
CG2 A:THR209 4.9 24.0 1.0

Fluorine binding site 2 out of 4 in 7g7j

Go back to Fluorine Binding Sites List in 7g7j
Fluorine binding site 2 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 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-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:32.4
occ:1.00
 F42 A:XSB901 0.0 32.4 1.0
C41 A:XSB901 1.3 29.8 1.0
F44 A:XSB901 2.0 32.0 1.0
F43 A:XSB901 2.1 28.9 1.0
C31 A:XSB901 2.4 28.5 1.0
C30 A:XSB901 3.1 32.7 1.0
C32 A:XSB901 3.4 27.4 1.0
CE2 A:PHE273 3.5 27.0 1.0
CG2 A:ILE167 3.6 19.3 1.0
CD1 A:ILE167 3.6 20.3 1.0
CD2 A:PHE273 3.8 24.1 1.0
CB A:ILE167 4.2 20.5 1.0
C29 A:XSB901 4.4 32.2 1.0
CG1 A:ILE167 4.4 20.5 1.0
C33 A:XSB901 4.6 28.2 1.0
CB A:ALA304 4.7 24.7 1.0
CZ A:PHE273 4.8 27.3 1.0
CE A:MET512 4.9 23.5 1.0
CB A:LEU216 4.9 21.1 1.0
C28 A:XSB901 5.0 29.3 1.0
SD A:MET512 5.0 25.6 1.0

Fluorine binding site 3 out of 4 in 7g7j

Go back to Fluorine Binding Sites List in 7g7j
Fluorine binding site 3 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 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-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:28.9
occ:1.00
 F43 A:XSB901 0.0 28.9 1.0
C41 A:XSB901 1.3 29.8 1.0
F44 A:XSB901 2.1 32.0 1.0
F42 A:XSB901 2.1 32.4 1.0
C31 A:XSB901 2.4 28.5 1.0
C32 A:XSB901 2.8 27.4 1.0
N A:ALA217 3.3 19.1 1.0
O A:LEU213 3.4 21.3 1.0
CB A:LEU216 3.5 21.1 1.0
CA A:ALA217 3.5 19.7 1.0
CB A:ALA217 3.6 19.4 1.0
C30 A:XSB901 3.6 32.7 1.0
C A:LEU216 3.7 19.9 1.0
C33 A:XSB901 4.2 28.2 1.0
CA A:LEU216 4.2 20.0 1.0
O A:LEU216 4.3 20.3 1.0
C A:LEU213 4.5 19.9 1.0
CD2 A:PHE273 4.7 24.1 1.0
CE2 A:PHE273 4.7 27.0 1.0
CG A:LEU216 4.8 23.3 1.0
C29 A:XSB901 4.8 32.2 1.0
CD1 A:LEU216 4.8 27.0 1.0
CA A:LEU213 5.0 19.8 1.0
C28 A:XSB901 5.0 29.3 1.0

Fluorine binding site 4 out of 4 in 7g7j

Go back to Fluorine Binding Sites List in 7g7j
Fluorine binding site 4 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 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 4-[(3AR,6AR)-2- [(E)-3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Prop-2-Enoyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]-3-Fluorobenzenesulfonamide, I.E. Smiles [C@@H]12CN(C(=O) C3C(Cc(CC3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/C1CCC(CC1CN1N=Nc(=N1) C)C(F)(F)F with IC50=0.00194649 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:32.0
occ:1.00
 F44 A:XSB901 0.0 32.0 1.0
C41 A:XSB901 1.3 29.8 1.0
F42 A:XSB901 2.0 32.4 1.0
F43 A:XSB901 2.1 28.9 1.0
C31 A:XSB901 2.4 28.5 1.0
C30 A:XSB901 2.9 32.7 1.0
C32 A:XSB901 3.6 27.4 1.0
CB A:LEU216 3.6 21.1 1.0
CD1 A:LEU216 3.8 27.0 1.0
CG2 A:ILE167 3.8 19.3 1.0
C29 A:XSB901 4.3 32.2 1.0
CG A:LEU216 4.3 23.3 1.0
CD2 A:LEU213 4.6 24.0 1.0
CB A:SER169 4.6 26.1 1.0
O A:LEU213 4.6 21.3 1.0
CG1 A:VAL356 4.7 19.9 1.0
C33 A:XSB901 4.7 28.2 1.0
N A:ALA217 4.9 19.1 1.0
C A:LEU216 4.9 19.9 1.0
CA A:LEU216 4.9 20.0 1.0
CB A:ILE167 5.0 20.5 1.0
OG A:SER169 5.0 31.2 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 18:05:15 2025

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