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Fluorine in PDB 7g78: Crystal Structure of Rat Autotaxin in Complex with 2-[6-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[6-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[6-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[6-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 Microm, PDB code: 7g78 was solved by M.Stihle, J.Benz, D.Hunziker, E.Martin-Rainer, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.31 / 1.91
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.646, 92.618, 120.88, 90, 90, 90
R / Rfree (%) 19.1 / 23.6

Other elements in 7g78:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[6-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 Microm also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 1 atom
Potassium (K) 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 2-[6-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 Microm (pdb code 7g78). 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 2-[6-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 Microm, PDB code: 7g78:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g78

Go back to Fluorine Binding Sites List in 7g78
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 2-[6-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 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 2-[6-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:52.0
occ:1.00
 F36 A:XSF901 0.0 52.0 1.0
C35 A:XSF901 1.3 53.2 1.0
F37 A:XSF901 2.2 52.9 1.0
F38 A:XSF901 2.2 53.0 1.0
O31 A:XSF901 2.3 47.6 1.0
C26 A:XSF901 2.9 41.5 1.0
O A:LEU213 3.2 23.6 1.0
CL30 A:XSF901 3.3 46.1 1.0
C27 A:XSF901 3.4 38.6 1.0
CB A:LEU213 3.7 21.3 1.0
C A:LEU213 3.9 21.4 1.0
C25 A:XSF901 3.9 37.1 1.0
CD2 A:LEU213 3.9 21.5 1.0
CA A:LEU213 3.9 21.7 1.0
CG A:LEU213 4.4 21.4 1.0
CB A:LEU216 4.4 24.4 1.0
C28 A:XSF901 4.6 39.7 1.0
CB A:ALA217 4.8 18.9 1.0
CD1 A:LEU216 4.8 34.4 1.0
CD2 A:PHE273 4.9 25.3 1.0
N A:ALA217 4.9 19.8 1.0
C24 A:XSF901 4.9 38.5 1.0
OG A:SER169 5.0 32.8 1.0

Fluorine binding site 2 out of 3 in 7g78

Go back to Fluorine Binding Sites List in 7g78
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 2-[6-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 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 2-[6-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:52.9
occ:1.00
 F37 A:XSF901 0.0 52.9 1.0
C35 A:XSF901 1.3 53.2 1.0
F38 A:XSF901 2.1 53.0 1.0
F36 A:XSF901 2.2 52.0 1.0
O31 A:XSF901 2.2 47.6 1.0
C26 A:XSF901 2.8 41.5 1.0
C25 A:XSF901 3.0 37.1 1.0
OG A:SER169 3.1 32.8 1.0
CB A:SER169 3.7 24.9 1.0
CD2 A:LEU213 3.9 21.5 1.0
C27 A:XSF901 3.9 38.6 1.0
C24 A:XSF901 4.2 38.5 1.0
CG A:LEU213 4.7 21.4 1.0
CB A:LEU213 4.7 21.3 1.0
CL30 A:XSF901 4.7 46.1 1.0
CD1 A:TYR306 4.7 28.5 1.0
CB A:ALA304 4.9 24.0 1.0
CD1 A:LEU213 4.9 24.0 1.0
O A:PHE273 4.9 32.5 1.0
C28 A:XSF901 4.9 39.7 1.0
C23 A:XSF901 4.9 36.5 1.0
CB A:TYR306 5.0 26.3 1.0

Fluorine binding site 3 out of 3 in 7g78

Go back to Fluorine Binding Sites List in 7g78
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 2-[6-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 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 2-[6-(1- Acetylpiperidin-4-Yl)-4-Oxoquinazolin-3-Yl]-N-[[4-Chloro-3- (Trifluoromethoxy)Phenyl]Methyl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O)N(C=N2)Cc(=O)N(C)CC1CC(C(CC1)Cl)Oc(F)(F)F) C1CCN(CC1)C(=O)C with IC50=0.0156427 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:53.0
occ:1.00
 F38 A:XSF901 0.0 53.0 1.0
C35 A:XSF901 1.3 53.2 1.0
F37 A:XSF901 2.1 52.9 1.0
F36 A:XSF901 2.2 52.0 1.0
O31 A:XSF901 2.3 47.6 1.0
CD2 A:PHE273 3.4 25.3 1.0
C26 A:XSF901 3.6 41.5 1.0
CE2 A:PHE273 4.0 25.4 1.0
CB A:ALA304 4.0 24.0 1.0
CG2 A:ILE167 4.2 25.9 1.0
C25 A:XSF901 4.3 37.1 1.0
CG A:PHE273 4.4 28.0 1.0
OG A:SER169 4.5 32.8 1.0
CB A:PHE273 4.6 28.0 1.0
C27 A:XSF901 4.6 38.6 1.0
CD1 A:ILE167 4.6 25.3 1.0
CL30 A:XSF901 4.7 46.1 1.0
CB A:ILE167 4.8 25.1 1.0
CB A:SER169 4.9 24.9 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: Sat Feb 8 18:05:15 2025

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