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Fluorine in PDB 7g2j: Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm, PDB code: 7g2j was solved by M.Stihle, J.Benz, D.Hunziker, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.86 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.275, 91.714, 119.828, 90, 90, 90
R / Rfree (%) 18.2 / 22.1

Other elements in 7g2j:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm (pdb code 7g2j). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm, PDB code: 7g2j:

Fluorine binding site 1 out of 1 in 7g2j

Go back to Fluorine Binding Sites List in 7g2j
Fluorine binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 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-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F907

b:47.1
occ:1.00
 F9 A:XHU907 0.0 47.1 1.0
C8 A:XHU907 1.4 44.0 1.0
C7 A:XHU907 2.3 45.3 1.0
C10 A:XHU907 2.4 35.7 1.0
C12 A:XHU907 2.8 29.1 1.0
C13 A:XHU907 2.9 28.1 1.0
N A:TYR214 3.0 19.2 1.0
C A:LEU213 3.0 19.5 1.0
CB A:LEU213 3.2 21.9 1.0
O A:LEU213 3.2 19.6 1.0
CA A:TYR214 3.3 20.7 1.0
C6 A:XHU907 3.6 47.8 1.0
C11 A:XHU907 3.7 40.0 1.0
CB A:TYR214 3.7 22.9 1.0
CA A:LEU213 3.7 21.4 1.0
CD1 A:TYR214 3.8 24.0 1.0
C20 A:XHU907 4.0 27.6 1.0
C14 A:XHU907 4.1 29.0 1.0
C5 A:XHU907 4.1 48.4 1.0
CG A:TYR214 4.2 23.4 1.0
O A:PHE210 4.5 24.4 1.0
O21 A:XHU907 4.5 27.8 1.0
CG A:LEU213 4.6 26.2 1.0
N A:LEU213 4.7 20.2 1.0
C A:TYR214 4.8 20.7 1.0
CD1 A:LEU213 4.8 27.0 1.0
CH2 A:TRP260 4.8 25.0 1.0
CD1 A:PHE210 4.8 41.1 1.0
CB A:ALA217 4.8 23.7 1.0
C15 A:XHU907 4.8 28.2 1.0
C19 A:XHU907 4.9 30.1 1.0
C17 A:XHU907 5.0 31.1 1.0
CE1 A:TYR214 5.0 25.3 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 19:54:27 2025

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