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Fluorine in PDB 7g3i: Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm, PDB code: 7g3i was solved by M.Stihle, J.Benz, D.Hunziker, E.Pinard, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.81 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.988, 91.306, 118.107, 90, 90, 90
R / Rfree (%) 17.2 / 21.2

Other elements in 7g3i:

The structure of Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 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 (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm (pdb code 7g3i). 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 (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm, PDB code: 7g3i:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g3i

Go back to Fluorine Binding Sites List in 7g3i
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 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 (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:27.7
occ:1.00
 F12 A:XET901 0.0 27.7 1.0
C11 A:XET901 1.3 26.3 1.0
F14 A:XET901 2.1 28.3 1.0
F13 A:XET901 2.1 26.9 1.0
O10 A:XET901 2.2 22.7 1.0
CE2 A:PHE274 3.3 55.8 1.0
CZ3 A:TRP254 3.4 23.8 1.0
C8 A:XET901 3.5 19.4 1.0
CD1 A:TYR214 3.8 15.7 1.0
CZ A:PHE274 3.9 54.3 1.0
CH2 A:TRP254 4.0 24.7 1.0
CH2 A:TRP260 4.1 23.0 1.0
CE3 A:TRP254 4.2 24.2 1.0
C7 A:XET901 4.3 19.3 1.0
C9 A:XET901 4.3 20.2 1.0
CD2 A:PHE274 4.4 52.9 1.0
CE1 A:TYR214 4.5 16.7 1.0
CG A:TYR214 4.6 16.1 1.0
CD1 A:PHE210 4.6 25.0 1.0
CB A:TYR214 4.6 16.5 1.0
CE1 A:PHE210 4.7 27.4 1.0
CZ2 A:TRP260 4.8 21.9 1.0
CA A:TYR214 4.9 15.7 1.0
CZ2 A:TRP254 5.0 22.9 1.0
CZ3 A:TRP260 5.0 23.5 1.0

Fluorine binding site 2 out of 3 in 7g3i

Go back to Fluorine Binding Sites List in 7g3i
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 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 (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:26.9
occ:1.00
 F13 A:XET901 0.0 26.9 1.0
C11 A:XET901 1.3 26.3 1.0
F14 A:XET901 2.0 28.3 1.0
F12 A:XET901 2.1 27.7 1.0
O10 A:XET901 2.2 22.7 1.0
C8 A:XET901 2.7 19.4 1.0
C7 A:XET901 3.0 19.3 1.0
CE1 A:PHE210 3.7 27.4 1.0
C9 A:XET901 3.7 20.2 1.0
CB A:LEU213 3.7 15.0 1.0
CD1 A:PHE210 3.7 25.0 1.0
CD1 A:LEU213 3.8 16.8 1.0
CE2 A:PHE274 3.9 55.8 1.0
C6 A:XET901 4.2 20.8 1.0
N22 A:XET901 4.3 21.8 1.0
CD2 A:PHE274 4.4 52.9 1.0
CG A:LEU213 4.4 16.1 1.0
C21 A:XET901 4.5 23.8 1.0
C4 A:XET901 4.7 20.1 1.0
C A:LEU213 4.8 13.5 1.0
CZ3 A:TRP254 4.8 23.8 1.0
CA A:LEU213 4.9 14.6 1.0
C5 A:XET901 4.9 19.2 1.0
C17 A:XET901 4.9 22.4 1.0
CZ A:PHE274 4.9 54.3 1.0
N A:TYR214 4.9 13.3 1.0
CZ A:PHE210 5.0 28.0 1.0

Fluorine binding site 3 out of 3 in 7g3i

Go back to Fluorine Binding Sites List in 7g3i
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 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 (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:28.3
occ:1.00
 F14 A:XET901 0.0 28.3 1.0
C11 A:XET901 1.3 26.3 1.0
F13 A:XET901 2.0 26.9 1.0
F12 A:XET901 2.1 27.7 1.0
O10 A:XET901 2.2 22.7 1.0
C8 A:XET901 2.8 19.4 1.0
C9 A:XET901 3.0 20.2 1.0
C A:LEU213 3.2 13.5 1.0
N A:TYR214 3.3 13.3 1.0
CB A:LEU213 3.3 15.0 1.0
O A:LEU213 3.4 13.5 1.0
CA A:TYR214 3.4 15.7 1.0
CB A:TYR214 3.7 16.5 1.0
CD1 A:TYR214 3.7 15.7 1.0
C7 A:XET901 3.8 19.3 1.0
CA A:LEU213 3.9 14.6 1.0
C4 A:XET901 4.2 20.1 1.0
CG A:TYR214 4.2 16.1 1.0
CZ3 A:TRP254 4.6 23.8 1.0
CG A:LEU213 4.6 16.1 1.0
O A:PHE210 4.7 19.3 1.0
CB A:ALA217 4.7 15.5 1.0
CD1 A:LEU213 4.7 16.8 1.0
CH2 A:TRP260 4.7 23.0 1.0
CD1 A:PHE210 4.7 25.0 1.0
C A:TYR214 4.8 15.2 1.0
C6 A:XET901 4.9 20.8 1.0
CE1 A:TYR214 4.9 16.7 1.0
N A:LEU213 4.9 15.3 1.0
CE2 A:PHE274 4.9 55.8 1.0
C5 A:XET901 5.0 19.2 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: Tue Jul 15 19:56:32 2025

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