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Fluorine in PDB 7g31: Crystal Structure of Rat Autotaxin in Complex with (3S)-3-(3- Bromophenyl)-3-[[2-[2-[(3,3-Difluoroazetidin-1-Yl)Methyl]-6- Methoxyphenoxy]Acetyl]Amino]-N-Methylpropanamide, I.E. Smiles FC1(F) Cn(CC2C(C(CCC2)Oc)Occ(=O)N[C@H](C2CC(CCC2)Br)Cc(=O)Nc)C1 with IC50=0.276983 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3S)-3-(3- Bromophenyl)-3-[[2-[2-[(3,3-Difluoroazetidin-1-Yl)Methyl]-6- Methoxyphenoxy]Acetyl]Amino]-N-Methylpropanamide, I.E. Smiles FC1(F) Cn(CC2C(C(CCC2)Oc)Occ(=O)N[C@H](C2CC(CCC2)Br)Cc(=O)Nc)C1 with IC50=0.276983 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3S)-3-(3- Bromophenyl)-3-[[2-[2-[(3,3-Difluoroazetidin-1-Yl)Methyl]-6- Methoxyphenoxy]Acetyl]Amino]-N-Methylpropanamide, I.E. Smiles FC1(F) Cn(CC2C(C(CCC2)Oc)Occ(=O)N[C@H](C2CC(CCC2)Br)Cc(=O)Nc)C1 with IC50=0.276983 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (3S)-3-(3- Bromophenyl)-3-[[2-[2-[(3,3-Difluoroazetidin-1-Yl)Methyl]-6- Methoxyphenoxy]Acetyl]Amino]-N-Methylpropanamide, I.E. Smiles FC1(F) Cn(CC2C(C(CCC2)Oc)Occ(=O)N[C@H](C2CC(CCC2)Br)Cc(=O)Nc)C1 with IC50=0.276983 Microm, PDB code: 7g31 was solved by M.Stihle, J.Benz, D.Hunziker, H.Kuhne, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.86 / 1.71
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.869, 91.719, 119.952, 90, 90, 90
R / Rfree (%) 18.9 / 22.4

Other elements in 7g31:

The structure of Crystal Structure of Rat Autotaxin in Complex with (3S)-3-(3- Bromophenyl)-3-[[2-[2-[(3,3-Difluoroazetidin-1-Yl)Methyl]-6- Methoxyphenoxy]Acetyl]Amino]-N-Methylpropanamide, I.E. Smiles FC1(F) Cn(CC2C(C(CCC2)Oc)Occ(=O)N[C@H](C2CC(CCC2)Br)Cc(=O)Nc)C1 with IC50=0.276983 Microm also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with (3S)-3-(3- Bromophenyl)-3-[[2-[2-[(3,3-Difluoroazetidin-1-Yl)Methyl]-6- Methoxyphenoxy]Acetyl]Amino]-N-Methylpropanamide, I.E. Smiles FC1(F) Cn(CC2C(C(CCC2)Oc)Occ(=O)N[C@H](C2CC(CCC2)Br)Cc(=O)Nc)C1 with IC50=0.276983 Microm (pdb code 7g31). 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 (3S)-3-(3- Bromophenyl)-3-[[2-[2-[(3,3-Difluoroazetidin-1-Yl)Methyl]-6- Methoxyphenoxy]Acetyl]Amino]-N-Methylpropanamide, I.E. Smiles FC1(F) Cn(CC2C(C(CCC2)Oc)Occ(=O)N[C@H](C2CC(CCC2)Br)Cc(=O)Nc)C1 with IC50=0.276983 Microm, PDB code: 7g31:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7g31

Go back to Fluorine Binding Sites List in 7g31
Fluorine binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (3S)-3-(3- Bromophenyl)-3-[[2-[2-[(3,3-Difluoroazetidin-1-Yl)Methyl]-6- Methoxyphenoxy]Acetyl]Amino]-N-Methylpropanamide, I.E. Smiles FC1(F) Cn(CC2C(C(CCC2)Oc)Occ(=O)N[C@H](C2CC(CCC2)Br)Cc(=O)Nc)C1 with IC50=0.276983 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 (3S)-3-(3- Bromophenyl)-3-[[2-[2-[(3,3-Difluoroazetidin-1-Yl)Methyl]-6- Methoxyphenoxy]Acetyl]Amino]-N-Methylpropanamide, I.E. Smiles FC1(F) Cn(CC2C(C(CCC2)Oc)Occ(=O)N[C@H](C2CC(CCC2)Br)Cc(=O)Nc)C1 with IC50=0.276983 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:17.7
occ:1.00
 FAA A:XEX901 0.0 17.7 1.0
CAB A:XEX901 1.4 17.9 1.0
FAC A:XEX901 2.2 19.7 1.0
CBF A:XEX901 2.5 16.9 1.0
CBG A:XEX901 2.5 16.0 1.0
CG2 A:ILE167 3.3 11.0 1.0
NBE A:XEX901 3.3 17.1 1.0
CB A:SER169 3.5 14.1 1.0
CD1 A:LEU216 3.7 12.6 1.0
CG1 A:VAL356 3.7 11.3 1.0
CB A:LEU216 4.0 10.3 1.0
OG A:SER169 4.0 16.2 1.0
CAX A:XEX901 4.4 15.3 1.0
CG A:LEU216 4.4 11.7 1.0
CB A:ILE167 4.6 13.1 1.0
CA A:SER169 4.8 13.9 1.0
CD2 A:LEU216 4.9 11.8 1.0

Fluorine binding site 2 out of 2 in 7g31

Go back to Fluorine Binding Sites List in 7g31
Fluorine binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (3S)-3-(3- Bromophenyl)-3-[[2-[2-[(3,3-Difluoroazetidin-1-Yl)Methyl]-6- Methoxyphenoxy]Acetyl]Amino]-N-Methylpropanamide, I.E. Smiles FC1(F) Cn(CC2C(C(CCC2)Oc)Occ(=O)N[C@H](C2CC(CCC2)Br)Cc(=O)Nc)C1 with IC50=0.276983 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 (3S)-3-(3- Bromophenyl)-3-[[2-[2-[(3,3-Difluoroazetidin-1-Yl)Methyl]-6- Methoxyphenoxy]Acetyl]Amino]-N-Methylpropanamide, I.E. Smiles FC1(F) Cn(CC2C(C(CCC2)Oc)Occ(=O)N[C@H](C2CC(CCC2)Br)Cc(=O)Nc)C1 with IC50=0.276983 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:19.7
occ:1.00
 FAC A:XEX901 0.0 19.7 1.0
CAB A:XEX901 1.4 17.9 1.0
FAA A:XEX901 2.2 17.7 1.0
CBG A:XEX901 2.4 16.0 1.0
CBF A:XEX901 2.5 16.9 1.0
NBE A:XEX901 2.8 17.1 1.0
CB A:LEU216 3.9 10.3 1.0
CG2 A:ILE167 4.0 11.0 1.0
N A:ALA217 4.2 10.9 1.0
C A:LEU216 4.2 12.0 1.0
CD1 A:ILE167 4.2 13.5 1.0
CE2 A:PHE273 4.2 13.3 1.0
CAX A:XEX901 4.3 15.3 1.0
CA A:ALA217 4.4 11.6 1.0
O A:LEU216 4.5 11.3 1.0
CD2 A:PHE273 4.5 13.6 1.0
CB A:ALA217 4.5 12.9 1.0
CE A:MET512 4.6 12.1 1.0
CA A:LEU216 4.7 10.6 1.0
CAV A:XEX901 4.8 16.6 1.0
CB A:ILE167 4.8 13.1 1.0
CD1 A:LEU216 4.8 12.6 1.0
SD A:MET512 4.8 16.0 1.0
O A:LEU213 4.8 9.4 1.0
CG A:LEU216 5.0 11.7 1.0
CG1 A:ILE167 5.0 12.0 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 17:51:55 2025

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