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Fluorine in PDB 7g6y: Crystal Structure of Rat Autotaxin in Complex with 1-[4-[[7-[(3,4- Difluorophenyl)Methyl]-9-Methyl-8-Oxopurin-2- Yl]Amino]Benzoyl]Piperidine-4-Sulfonamide, I.E. Smiles C1NC(NC2C1N(C(=O)N2C)CC1CCC(C(C1)F)F)NC1CCC(CC1)C(=O)N1CCC(CC1)S(=O) (=O)N with IC50=0.00233021 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1-[4-[[7-[(3,4- Difluorophenyl)Methyl]-9-Methyl-8-Oxopurin-2- Yl]Amino]Benzoyl]Piperidine-4-Sulfonamide, I.E. Smiles C1NC(NC2C1N(C(=O)N2C)CC1CCC(C(C1)F)F)NC1CCC(CC1)C(=O)N1CCC(CC1)S(=O) (=O)N with IC50=0.00233021 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1-[4-[[7-[(3,4- Difluorophenyl)Methyl]-9-Methyl-8-Oxopurin-2- Yl]Amino]Benzoyl]Piperidine-4-Sulfonamide, I.E. Smiles C1NC(NC2C1N(C(=O)N2C)CC1CCC(C(C1)F)F)NC1CCC(CC1)C(=O)N1CCC(CC1)S(=O) (=O)N with IC50=0.00233021 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 1-[4-[[7-[(3,4- Difluorophenyl)Methyl]-9-Methyl-8-Oxopurin-2- Yl]Amino]Benzoyl]Piperidine-4-Sulfonamide, I.E. Smiles C1NC(NC2C1N(C(=O)N2C)CC1CCC(C(C1)F)F)NC1CCC(CC1)C(=O)N1CCC(CC1)S(=O) (=O)N with IC50=0.00233021 Microm, PDB code: 7g6y 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) 48.90 / 1.48
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.007, 92.008, 120.287, 90, 90, 90
R / Rfree (%) 18.2 / 20.9

Other elements in 7g6y:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1-[4-[[7-[(3,4- Difluorophenyl)Methyl]-9-Methyl-8-Oxopurin-2- Yl]Amino]Benzoyl]Piperidine-4-Sulfonamide, I.E. Smiles C1NC(NC2C1N(C(=O)N2C)CC1CCC(C(C1)F)F)NC1CCC(CC1)C(=O)N1CCC(CC1)S(=O) (=O)N with IC50=0.00233021 Microm also contains other interesting chemical elements:

Sodium (Na) 1 atom
Calcium (Ca) 1 atom
Potassium (K) 1 atom
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 1-[4-[[7-[(3,4- Difluorophenyl)Methyl]-9-Methyl-8-Oxopurin-2- Yl]Amino]Benzoyl]Piperidine-4-Sulfonamide, I.E. Smiles C1NC(NC2C1N(C(=O)N2C)CC1CCC(C(C1)F)F)NC1CCC(CC1)C(=O)N1CCC(CC1)S(=O) (=O)N with IC50=0.00233021 Microm (pdb code 7g6y). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Rat Autotaxin in Complex with 1-[4-[[7-[(3,4- Difluorophenyl)Methyl]-9-Methyl-8-Oxopurin-2- Yl]Amino]Benzoyl]Piperidine-4-Sulfonamide, I.E. Smiles C1NC(NC2C1N(C(=O)N2C)CC1CCC(C(C1)F)F)NC1CCC(CC1)C(=O)N1CCC(CC1)S(=O) (=O)N with IC50=0.00233021 Microm, PDB code: 7g6y:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7g6y

Go back to Fluorine Binding Sites List in 7g6y
Fluorine binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1-[4-[[7-[(3,4- Difluorophenyl)Methyl]-9-Methyl-8-Oxopurin-2- Yl]Amino]Benzoyl]Piperidine-4-Sulfonamide, I.E. Smiles C1NC(NC2C1N(C(=O)N2C)CC1CCC(C(C1)F)F)NC1CCC(CC1)C(=O)N1CCC(CC1)S(=O) (=O)N with IC50=0.00233021 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 1-[4-[[7-[(3,4- Difluorophenyl)Methyl]-9-Methyl-8-Oxopurin-2- Yl]Amino]Benzoyl]Piperidine-4-Sulfonamide, I.E. Smiles C1NC(NC2C1N(C(=O)N2C)CC1CCC(C(C1)F)F)NC1CCC(CC1)C(=O)N1CCC(CC1)S(=O) (=O)N with IC50=0.00233021 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:22.7
occ:1.00
 F34 A:Y4W901 0.0 22.7 1.0
C18 A:Y4W901 1.4 18.6 1.0
C17 A:Y4W901 2.3 18.8 1.0
C19 A:Y4W901 2.5 17.5 1.0
F35 A:Y4W901 2.7 21.3 1.0
OG A:SER169 2.9 18.6 1.0
O A:PHE305 3.4 16.6 1.0
CB A:ALA304 3.4 17.0 1.0
CB A:SER169 3.5 15.6 1.0
C14 A:Y4W901 3.7 18.4 1.0
C16 A:Y4W901 3.7 17.9 1.0
CG2 A:ILE167 3.8 15.2 1.0
C A:PHE305 4.2 15.8 1.0
C15 A:Y4W901 4.2 17.9 1.0
O A:ILE167 4.3 16.5 1.0
N A:PHE305 4.3 16.0 1.0
N A:SER169 4.4 14.0 1.0
CB A:ILE167 4.4 14.5 1.0
CA A:ALA304 4.4 14.9 1.0
CA A:SER169 4.6 13.8 1.0
C A:ALA304 4.6 16.3 1.0
CB A:TYR306 4.7 17.3 1.0
C A:ILE167 4.8 14.8 1.0
N A:TYR306 4.8 15.8 1.0
CD2 A:PHE273 4.9 19.6 1.0
CA A:TYR306 4.9 16.8 1.0
O A:PHE273 4.9 23.3 1.0
CA A:PHE305 5.0 14.7 1.0

Fluorine binding site 2 out of 2 in 7g6y

Go back to Fluorine Binding Sites List in 7g6y
Fluorine binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1-[4-[[7-[(3,4- Difluorophenyl)Methyl]-9-Methyl-8-Oxopurin-2- Yl]Amino]Benzoyl]Piperidine-4-Sulfonamide, I.E. Smiles C1NC(NC2C1N(C(=O)N2C)CC1CCC(C(C1)F)F)NC1CCC(CC1)C(=O)N1CCC(CC1)S(=O) (=O)N with IC50=0.00233021 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 1-[4-[[7-[(3,4- Difluorophenyl)Methyl]-9-Methyl-8-Oxopurin-2- Yl]Amino]Benzoyl]Piperidine-4-Sulfonamide, I.E. Smiles C1NC(NC2C1N(C(=O)N2C)CC1CCC(C(C1)F)F)NC1CCC(CC1)C(=O)N1CCC(CC1)S(=O) (=O)N with IC50=0.00233021 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:21.3
occ:1.00
 F35 A:Y4W901 0.0 21.3 1.0
C17 A:Y4W901 1.3 18.8 1.0
C18 A:Y4W901 2.4 18.6 1.0
C16 A:Y4W901 2.4 17.9 1.0
F34 A:Y4W901 2.7 22.7 1.0
CG2 A:ILE167 3.3 15.2 1.0
CB A:SER169 3.5 15.6 1.0
C15 A:Y4W901 3.6 17.9 1.0
C19 A:Y4W901 3.7 17.5 1.0
OG A:SER169 3.8 18.6 1.0
C14 A:Y4W901 4.1 18.4 1.0
CD1 A:LEU216 4.2 17.2 1.0
CG1 A:VAL356 4.3 13.9 1.0
CB A:LEU216 4.4 12.3 1.0
CD2 A:LEU213 4.5 16.1 1.0
CB A:ILE167 4.6 14.5 1.0
CA A:SER169 4.8 13.8 1.0
CG A:LEU216 4.9 14.5 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 20:03:43 2025

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