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Fluorine in PDB 7g65: Crystal Structure of Rat Autotaxin in Complex with 4-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide, PDB code: 7g65 was solved by M.Stihle, J.Benz, D.Hunziker, K.Hada, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.81 / 1.73
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.777, 91.623, 118.712, 90, 90, 90
R / Rfree (%) 18.5 / 21.7

Other elements in 7g65:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with 4-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide (pdb code 7g65). 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 4-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide, PDB code: 7g65:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g65

Go back to Fluorine Binding Sites List in 7g65
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 4-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide


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-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F906

b:36.4
occ:1.00
 F21 A:YBB906 0.0 36.4 1.0
C20 A:YBB906 1.4 39.6 1.0
O7 A:YBB906 2.2 36.7 1.0
F22 A:YBB906 2.2 38.2 1.0
F23 A:YBB906 2.2 32.8 1.0
SD A:MET512 3.1 18.9 1.0
CE A:MET512 3.1 17.9 1.0
C2 A:YBB906 3.5 37.2 1.0
CG2 A:ILE167 3.5 18.7 1.0
CB A:LEU216 4.0 15.9 1.0
CG1 A:ILE167 4.1 19.4 1.0
O A:LEU216 4.2 16.9 1.0
C1 A:YBB906 4.2 32.3 1.0
CD1 A:ILE167 4.3 22.2 1.0
C3 A:YBB906 4.4 36.8 1.0
CB A:ILE167 4.4 19.2 1.0
C A:LEU216 4.4 16.2 1.0
CG1 A:VAL356 4.6 14.6 1.0
CD2 A:LEU216 4.6 18.4 1.0
CG A:LEU216 4.8 17.7 1.0
CA A:LEU216 4.8 15.3 1.0
CG A:MET512 4.9 15.8 1.0
CD1 A:LEU216 4.9 20.5 1.0
N A:ALA217 5.0 16.0 1.0

Fluorine binding site 2 out of 3 in 7g65

Go back to Fluorine Binding Sites List in 7g65
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 4-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide


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-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F906

b:38.2
occ:1.00
 F22 A:YBB906 0.0 38.2 1.0
C20 A:YBB906 1.3 39.6 1.0
F23 A:YBB906 2.1 32.8 1.0
F21 A:YBB906 2.2 36.4 1.0
O7 A:YBB906 2.2 36.7 1.0
C2 A:YBB906 2.8 37.2 1.0
CD1 A:ILE167 3.0 22.2 1.0
C3 A:YBB906 3.3 36.8 1.0
CG2 A:ILE167 3.3 18.7 1.0
CG1 A:ILE167 3.4 19.4 1.0
CE2 A:PHE273 3.6 29.8 1.0
CB A:ILE167 3.6 19.2 1.0
C1 A:YBB906 3.6 32.3 1.0
SD A:MET512 3.9 18.9 1.0
CD2 A:PHE273 4.1 28.9 1.0
CE A:MET512 4.2 17.9 1.0
C4 A:YBB906 4.4 34.3 1.0
CZ A:PHE273 4.5 30.0 1.0
CD2 A:LEU259 4.6 17.1 1.0
C6 A:YBB906 4.7 32.8 1.0
C5 A:YBB906 5.0 33.1 1.0

Fluorine binding site 3 out of 3 in 7g65

Go back to Fluorine Binding Sites List in 7g65
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 4-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide


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-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F906

b:32.8
occ:1.00
 F23 A:YBB906 0.0 32.8 1.0
C20 A:YBB906 1.3 39.6 1.0
F22 A:YBB906 2.1 38.2 1.0
O7 A:YBB906 2.2 36.7 1.0
F21 A:YBB906 2.2 36.4 1.0
C2 A:YBB906 2.8 37.2 1.0
C1 A:YBB906 2.9 32.3 1.0
CA A:ALA217 3.4 16.2 1.0
C A:LEU216 3.4 16.2 1.0
N A:ALA217 3.4 16.0 1.0
O A:LEU216 3.5 16.9 1.0
CE A:MET512 3.7 17.9 1.0
CB A:LEU216 3.8 15.9 1.0
CB A:ALA217 3.8 17.4 1.0
C3 A:YBB906 4.0 36.8 1.0
C6 A:YBB906 4.1 32.8 1.0
CA A:LEU216 4.2 15.3 1.0
SD A:MET512 4.3 18.9 1.0
CE2 A:PHE273 4.5 29.8 1.0
C A:ALA217 4.7 16.1 1.0
O A:LEU213 4.8 15.2 1.0
C4 A:YBB906 4.9 34.3 1.0
CD1 A:ILE167 4.9 22.2 1.0
CD2 A:PHE273 4.9 28.9 1.0
C5 A:YBB906 4.9 33.1 1.0
CG2 A:ILE167 5.0 18.7 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 18:05:15 2025

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