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Fluorine in PDB 7g2s: Crystal Structure of Rat Autotaxin in Complex with 4-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 Microm, PDB code: 7g2s 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) 48.79 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.01, 91.702, 119.881, 90, 90, 90
R / Rfree (%) 21.6 / 26.3

Other elements in 7g2s:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 Microm also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Sodium (Na) 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-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 Microm (pdb code 7g2s). 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-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 Microm, PDB code: 7g2s:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g2s

Go back to Fluorine Binding Sites List in 7g2s
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 4-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 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-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:32.7
occ:1.00
 F3 A:XQR901 0.0 32.7 1.0
C2 A:XQR901 1.4 31.5 1.0
F4 A:XQR901 2.2 37.6 1.0
F5 A:XQR901 2.2 36.7 1.0
C1 A:XQR901 2.3 26.1 1.0
C35 A:XQR901 3.0 21.6 1.0
C6 A:XQR901 3.4 24.8 1.0
CB A:SER169 3.5 19.3 1.0
CD1 A:LEU216 3.8 19.1 1.0
CG2 A:ILE167 3.8 20.0 1.0
OG A:SER169 3.9 23.4 1.0
CD2 A:LEU213 4.0 20.0 1.0
CB A:LEU216 4.2 15.4 1.0
CG1 A:VAL356 4.2 17.9 1.0
C34 A:XQR901 4.3 22.8 1.0
CG A:LEU216 4.5 17.2 1.0
C7 A:XQR901 4.5 22.0 1.0
CA A:SER169 4.7 18.4 1.0
C8 A:XQR901 4.9 22.3 1.0
CB A:ILE167 5.0 20.2 1.0

Fluorine binding site 2 out of 3 in 7g2s

Go back to Fluorine Binding Sites List in 7g2s
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 4-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 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-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:37.6
occ:1.00
 F4 A:XQR901 0.0 37.6 1.0
C2 A:XQR901 1.3 31.5 1.0
F5 A:XQR901 2.0 36.7 1.0
F3 A:XQR901 2.2 32.7 1.0
C1 A:XQR901 2.3 26.1 1.0
C6 A:XQR901 2.6 24.8 1.0
OG A:SER169 3.1 23.4 1.0
CB A:SER169 3.2 19.3 1.0
CG2 A:ILE167 3.3 20.0 1.0
C35 A:XQR901 3.6 21.6 1.0
C7 A:XQR901 3.9 22.0 1.0
CB A:ALA304 3.9 18.3 1.0
CB A:ILE167 3.9 20.2 1.0
O A:PHE305 4.1 18.7 1.0
N A:SER169 4.2 16.1 1.0
O A:ILE167 4.2 18.9 1.0
CA A:SER169 4.2 18.4 1.0
C A:ILE167 4.5 19.0 1.0
C34 A:XQR901 4.7 22.8 1.0
C8 A:XQR901 4.8 22.3 1.0
CA A:ALA304 4.9 18.3 1.0
CA A:ILE167 4.9 17.5 1.0
CD2 A:PHE273 4.9 21.3 1.0

Fluorine binding site 3 out of 3 in 7g2s

Go back to Fluorine Binding Sites List in 7g2s
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 4-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 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-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:36.7
occ:1.00
 F5 A:XQR901 0.0 36.7 1.0
C2 A:XQR901 1.3 31.5 1.0
F4 A:XQR901 2.0 37.6 1.0
F3 A:XQR901 2.2 32.7 1.0
C1 A:XQR901 2.3 26.1 1.0
C35 A:XQR901 3.0 21.6 1.0
CG2 A:ILE167 3.1 20.0 1.0
C6 A:XQR901 3.3 24.8 1.0
CB A:ILE167 3.7 20.2 1.0
CD1 A:ILE167 3.8 24.0 1.0
CE2 A:PHE273 3.9 25.3 1.0
CD2 A:PHE273 4.1 21.3 1.0
CG1 A:ILE167 4.2 20.5 1.0
C34 A:XQR901 4.3 22.8 1.0
CB A:ALA304 4.3 18.3 1.0
C7 A:XQR901 4.4 22.0 1.0
C8 A:XQR901 4.8 22.3 1.0
CZ A:PHE273 5.0 23.8 1.0
CB A:SER169 5.0 19.3 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 19:55:36 2025

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