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Sodium in PDB 7g3c: Crystal Structure of Rat Autotaxin in Complex with 2-(3,4- Dichlorophenyl)-1-[8-[(4-Fluorophenyl)Methyl]-3,4-Dihydro-1H- Isoquinolin-2-Yl]Ethanone, I.E. Smiles FC1CCC(CC1)CC1C2CN(C(=O) CC3CCC(Cl)C(Cl)C3)CCC2CCC1 with IC50=0.769073 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-(3,4- Dichlorophenyl)-1-[8-[(4-Fluorophenyl)Methyl]-3,4-Dihydro-1H- Isoquinolin-2-Yl]Ethanone, I.E. Smiles FC1CCC(CC1)CC1C2CN(C(=O) CC3CCC(Cl)C(Cl)C3)CCC2CCC1 with IC50=0.769073 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-(3,4- Dichlorophenyl)-1-[8-[(4-Fluorophenyl)Methyl]-3,4-Dihydro-1H- Isoquinolin-2-Yl]Ethanone, I.E. Smiles FC1CCC(CC1)CC1C2CN(C(=O) CC3CCC(Cl)C(Cl)C3)CCC2CCC1 with IC50=0.769073 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-(3,4- Dichlorophenyl)-1-[8-[(4-Fluorophenyl)Methyl]-3,4-Dihydro-1H- Isoquinolin-2-Yl]Ethanone, I.E. Smiles FC1CCC(CC1)CC1C2CN(C(=O) CC3CCC(Cl)C(Cl)C3)CCC2CCC1 with IC50=0.769073 Microm, PDB code: 7g3c 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) 45.73 / 1.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.71, 91.46, 119.21, 90, 90, 90
R / Rfree (%) 17.3 / 20.5

Other elements in 7g3c:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-(3,4- Dichlorophenyl)-1-[8-[(4-Fluorophenyl)Methyl]-3,4-Dihydro-1H- Isoquinolin-2-Yl]Ethanone, I.E. Smiles FC1CCC(CC1)CC1C2CN(C(=O) CC3CCC(Cl)C(Cl)C3)CCC2CCC1 with IC50=0.769073 Microm also contains other interesting chemical elements:

Fluorine (F) 1 atom
Calcium (Ca) 2 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 2-(3,4- Dichlorophenyl)-1-[8-[(4-Fluorophenyl)Methyl]-3,4-Dihydro-1H- Isoquinolin-2-Yl]Ethanone, I.E. Smiles FC1CCC(CC1)CC1C2CN(C(=O) CC3CCC(Cl)C(Cl)C3)CCC2CCC1 with IC50=0.769073 Microm (pdb code 7g3c). 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 2-(3,4- Dichlorophenyl)-1-[8-[(4-Fluorophenyl)Methyl]-3,4-Dihydro-1H- Isoquinolin-2-Yl]Ethanone, I.E. Smiles FC1CCC(CC1)CC1C2CN(C(=O) CC3CCC(Cl)C(Cl)C3)CCC2CCC1 with IC50=0.769073 Microm, PDB code: 7g3c:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g3c

Go back to Sodium Binding Sites List in 7g3c
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-(3,4- Dichlorophenyl)-1-[8-[(4-Fluorophenyl)Methyl]-3,4-Dihydro-1H- Isoquinolin-2-Yl]Ethanone, I.E. Smiles FC1CCC(CC1)CC1C2CN(C(=O) CC3CCC(Cl)C(Cl)C3)CCC2CCC1 with IC50=0.769073 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 2-(3,4- Dichlorophenyl)-1-[8-[(4-Fluorophenyl)Methyl]-3,4-Dihydro-1H- Isoquinolin-2-Yl]Ethanone, I.E. Smiles FC1CCC(CC1)CC1C2CN(C(=O) CC3CCC(Cl)C(Cl)C3)CCC2CCC1 with IC50=0.769073 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:25.4
occ:1.00
 O A:HOH1291 2.3 26.3 1.0
OG A:SER807 2.3 24.5 1.0
O A:HOH1398 2.4 30.9 1.0
O A:SER804 2.4 21.0 1.0
O A:HOH1327 2.4 27.7 1.0
O A:ASN801 2.5 20.5 1.0
C A:ASN801 3.3 21.2 1.0
C A:SER804 3.4 22.5 1.0
CB A:SER807 3.5 24.9 1.0
CA A:ASP802 3.8 24.0 1.0
N A:ASP802 3.9 21.1 1.0
N A:SER807 4.1 26.4 1.0
O A:ASP802 4.1 21.6 1.0
C A:ASP802 4.2 22.5 1.0
CA A:CYS805 4.2 25.9 1.0
N A:CYS805 4.2 22.8 1.0
N A:SER804 4.3 20.3 1.0
CA A:SER807 4.3 26.6 1.0
CA A:SER804 4.3 20.5 1.0
CB A:ASN801 4.4 21.4 1.0
C A:CYS805 4.4 27.2 1.0
CA A:ASN801 4.4 20.7 1.0
O A:HOH1166 4.4 36.7 1.0
O A:CYS805 4.5 28.0 1.0
O A:HOH1161 4.7 30.6 1.0
OD1 A:ASP802 4.7 32.7 1.0
CB A:SER804 4.7 21.8 1.0
N A:ASN806 4.9 25.8 1.0
O A:HOH1303 4.9 33.7 1.0
N A:GLU803 5.0 19.5 1.0

Sodium binding site 2 out of 2 in 7g3c

Go back to Sodium Binding Sites List in 7g3c
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-(3,4- Dichlorophenyl)-1-[8-[(4-Fluorophenyl)Methyl]-3,4-Dihydro-1H- Isoquinolin-2-Yl]Ethanone, I.E. Smiles FC1CCC(CC1)CC1C2CN(C(=O) CC3CCC(Cl)C(Cl)C3)CCC2CCC1 with IC50=0.769073 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 2-(3,4- Dichlorophenyl)-1-[8-[(4-Fluorophenyl)Methyl]-3,4-Dihydro-1H- Isoquinolin-2-Yl]Ethanone, I.E. Smiles FC1CCC(CC1)CC1C2CN(C(=O) CC3CCC(Cl)C(Cl)C3)CCC2CCC1 with IC50=0.769073 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na911

b:24.1
occ:1.00
 O A:TYR669 2.3 29.4 1.0
O A:MET675 2.3 26.0 1.0
O A:ASP672 2.3 28.0 1.0
O A:HOH1357 2.4 31.4 1.0
O A:HOH1394 2.4 48.0 1.0
O A:HOH1416 2.7 39.6 1.0
C A:TYR669 3.4 30.2 1.0
C A:MET675 3.4 24.0 1.0
C A:ASP672 3.5 28.5 1.0
N A:MET675 4.1 25.3 1.0
CA A:TYR669 4.2 25.8 1.0
N A:SER676 4.3 21.6 1.0
CA A:MET675 4.3 24.7 1.0
CA A:LYS673 4.3 32.9 1.0
O A:LYS670 4.4 31.6 1.0
N A:LYS673 4.4 29.1 1.0
CA A:SER676 4.4 21.6 1.0
CA A:ASP672 4.4 27.4 1.0
N A:LYS670 4.4 29.6 1.0
C A:LYS673 4.5 30.6 1.0
N A:ASP672 4.5 28.6 1.0
CB A:TYR669 4.6 24.9 1.0
O A:LYS673 4.6 32.0 1.0
O A:HOH1442 4.6 45.0 1.0
CA A:LYS670 4.6 32.7 1.0
CB A:ASP672 4.6 28.4 1.0
C A:LYS670 4.6 29.6 1.0
N A:GLN674 4.9 28.9 1.0
CB A:MET675 4.9 22.9 1.0
CB A:SER676 5.0 22.1 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 23:12:39 2025

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