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Sodium 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
Bromine (Br) 2 atoms
Fluorine (F) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g31

Go back to Sodium Binding Sites List in 7g31
Sodium 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 Sodium with other atoms in the Na 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:Na906

b:23.0
occ:1.00
 OG A:SER807 2.3 16.9 1.0
O A:HOH1493 2.4 23.5 1.0
O A:HOH1397 2.4 23.1 1.0
O A:ASN801 2.4 14.8 1.0
O A:SER804 2.4 15.4 1.0
O A:HOH1314 2.5 22.4 1.0
C A:ASN801 3.3 15.9 1.0
CB A:SER807 3.4 15.5 1.0
C A:SER804 3.5 14.8 1.0
CA A:ASP802 3.9 17.4 1.0
O A:HOH1534 3.9 31.7 1.0
N A:ASP802 3.9 15.2 1.0
N A:SER807 4.1 19.6 1.0
O A:HOH1112 4.2 23.8 1.0
CA A:SER807 4.2 19.5 1.0
CA A:CYS805 4.3 17.5 1.0
C A:ASP802 4.3 18.2 1.0
CB A:ASN801 4.3 14.9 1.0
O A:ASP802 4.3 16.0 1.0
N A:CYS805 4.3 16.3 1.0
CA A:ASN801 4.3 14.2 1.0
N A:SER804 4.3 13.5 1.0
CA A:SER804 4.4 14.2 1.0
C A:CYS805 4.4 18.6 1.0
O A:CYS805 4.5 19.3 1.0
CB A:SER804 4.7 14.7 1.0
O A:HOH1066 4.7 30.3 1.0
OD1 A:ASP802 4.7 28.1 1.0
O A:HOH1349 5.0 27.1 1.0
N A:ASN806 5.0 17.8 1.0

Sodium binding site 2 out of 2 in 7g31

Go back to Sodium Binding Sites List in 7g31
Sodium 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 Sodium with other atoms in the Na 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:Na908

b:10.9
occ:1.00
 O A:ASP672 2.3 18.7 1.0
O A:HOH1469 2.3 38.9 1.0
O A:MET675 2.3 18.7 1.0
O A:TYR669 2.3 21.1 1.0
O A:HOH1476 2.3 32.6 1.0
O A:HOH1399 2.4 21.2 1.0
C A:MET675 3.4 17.5 1.0
C A:TYR669 3.4 20.7 1.0
C A:ASP672 3.5 20.0 1.0
N A:MET675 4.1 17.9 1.0
CA A:TYR669 4.2 18.6 1.0
O A:HOH1512 4.3 32.2 1.0
N A:SER676 4.3 15.9 1.0
CA A:MET675 4.3 16.8 1.0
CA A:LYS673 4.3 22.9 1.0
O A:LYS670 4.3 24.2 1.0
CA A:SER676 4.4 16.3 1.0
N A:LYS673 4.4 21.0 1.0
N A:LYS670 4.4 20.9 1.0
CA A:ASP672 4.5 20.6 1.0
C A:LYS673 4.5 22.0 1.0
N A:ASP672 4.5 21.4 1.0
C A:LYS670 4.6 21.6 1.0
CA A:LYS670 4.6 23.9 1.0
CB A:TYR669 4.6 17.3 1.0
CB A:ASP672 4.7 20.4 1.0
O A:LYS673 4.7 24.9 1.0
N A:GLN674 4.9 21.5 1.0
CB A:SER676 5.0 16.7 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 23:11:46 2025

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