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Sodium in PDB 7g2e: Crystal Structure of Rat Autotaxin in Complex with 2-(3,4- Dichlorophenyl)-1-[4-[(4-Fluorophenyl)Methyl]-7,8-Dihydro-5H- Pyrido[4,3-D]Pyrimidin-6-Yl]Ethanone, I.E. Smiles FC1CCC(CC1) CC1C2CN(C(=O)CC3CCC(Cl)C(Cl)C3)CCC2NCN1 with IC50=0.795943 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-(3,4- Dichlorophenyl)-1-[4-[(4-Fluorophenyl)Methyl]-7,8-Dihydro-5H- Pyrido[4,3-D]Pyrimidin-6-Yl]Ethanone, I.E. Smiles FC1CCC(CC1) CC1C2CN(C(=O)CC3CCC(Cl)C(Cl)C3)CCC2NCN1 with IC50=0.795943 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-(3,4- Dichlorophenyl)-1-[4-[(4-Fluorophenyl)Methyl]-7,8-Dihydro-5H- Pyrido[4,3-D]Pyrimidin-6-Yl]Ethanone, I.E. Smiles FC1CCC(CC1) CC1C2CN(C(=O)CC3CCC(Cl)C(Cl)C3)CCC2NCN1 with IC50=0.795943 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-(3,4- Dichlorophenyl)-1-[4-[(4-Fluorophenyl)Methyl]-7,8-Dihydro-5H- Pyrido[4,3-D]Pyrimidin-6-Yl]Ethanone, I.E. Smiles FC1CCC(CC1) CC1C2CN(C(=O)CC3CCC(Cl)C(Cl)C3)CCC2NCN1 with IC50=0.795943 Microm, PDB code: 7g2e 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) 45.71 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.58, 91.41, 119.16, 90, 90, 90
R / Rfree (%) 18.1 / 21.4

Other elements in 7g2e:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-(3,4- Dichlorophenyl)-1-[4-[(4-Fluorophenyl)Methyl]-7,8-Dihydro-5H- Pyrido[4,3-D]Pyrimidin-6-Yl]Ethanone, I.E. Smiles FC1CCC(CC1) CC1C2CN(C(=O)CC3CCC(Cl)C(Cl)C3)CCC2NCN1 with IC50=0.795943 Microm also contains other interesting chemical elements:

Fluorine (F) 1 atom
Zinc (Zn) 1 atom
Chlorine (Cl) 2 atoms
Calcium (Ca) 2 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-[4-[(4-Fluorophenyl)Methyl]-7,8-Dihydro-5H- Pyrido[4,3-D]Pyrimidin-6-Yl]Ethanone, I.E. Smiles FC1CCC(CC1) CC1C2CN(C(=O)CC3CCC(Cl)C(Cl)C3)CCC2NCN1 with IC50=0.795943 Microm (pdb code 7g2e). 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-[4-[(4-Fluorophenyl)Methyl]-7,8-Dihydro-5H- Pyrido[4,3-D]Pyrimidin-6-Yl]Ethanone, I.E. Smiles FC1CCC(CC1) CC1C2CN(C(=O)CC3CCC(Cl)C(Cl)C3)CCC2NCN1 with IC50=0.795943 Microm, PDB code: 7g2e:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g2e

Go back to Sodium Binding Sites List in 7g2e
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-(3,4- Dichlorophenyl)-1-[4-[(4-Fluorophenyl)Methyl]-7,8-Dihydro-5H- Pyrido[4,3-D]Pyrimidin-6-Yl]Ethanone, I.E. Smiles FC1CCC(CC1) CC1C2CN(C(=O)CC3CCC(Cl)C(Cl)C3)CCC2NCN1 with IC50=0.795943 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-[4-[(4-Fluorophenyl)Methyl]-7,8-Dihydro-5H- Pyrido[4,3-D]Pyrimidin-6-Yl]Ethanone, I.E. Smiles FC1CCC(CC1) CC1C2CN(C(=O)CC3CCC(Cl)C(Cl)C3)CCC2NCN1 with IC50=0.795943 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:27.4
occ:1.00
 O A:HOH1283 2.3 25.7 1.0
O A:HOH1383 2.3 32.0 1.0
OG A:SER807 2.3 22.4 1.0
O A:HOH1190 2.4 26.7 1.0
O A:SER804 2.5 20.4 1.0
O A:ASN801 2.5 19.2 1.0
C A:ASN801 3.4 19.4 1.0
CB A:SER807 3.5 23.6 1.0
C A:SER804 3.5 21.0 1.0
CA A:ASP802 3.8 23.1 1.0
N A:ASP802 3.9 21.6 1.0
O A:ASP802 4.2 21.6 1.0
N A:SER807 4.2 25.3 1.0
C A:ASP802 4.2 22.4 1.0
CA A:CYS805 4.2 27.2 1.0
O A:HOH1097 4.3 38.5 1.0
N A:CYS805 4.3 22.9 1.0
N A:SER804 4.4 20.7 1.0
CA A:SER807 4.4 26.0 1.0
C A:CYS805 4.4 25.9 1.0
CB A:ASN801 4.4 19.2 1.0
CA A:ASN801 4.4 19.3 1.0
O A:CYS805 4.4 27.3 1.0
CA A:SER804 4.4 20.0 1.0
OD1 A:ASP802 4.6 31.4 1.0
O A:HOH1063 4.7 30.7 1.0
O A:HOH1125 4.8 35.6 1.0
CB A:SER804 4.8 21.1 1.0
N A:ASN806 4.9 26.1 1.0
N A:GLU803 5.0 19.4 1.0

Sodium binding site 2 out of 2 in 7g2e

Go back to Sodium Binding Sites List in 7g2e
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-(3,4- Dichlorophenyl)-1-[4-[(4-Fluorophenyl)Methyl]-7,8-Dihydro-5H- Pyrido[4,3-D]Pyrimidin-6-Yl]Ethanone, I.E. Smiles FC1CCC(CC1) CC1C2CN(C(=O)CC3CCC(Cl)C(Cl)C3)CCC2NCN1 with IC50=0.795943 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-[4-[(4-Fluorophenyl)Methyl]-7,8-Dihydro-5H- Pyrido[4,3-D]Pyrimidin-6-Yl]Ethanone, I.E. Smiles FC1CCC(CC1) CC1C2CN(C(=O)CC3CCC(Cl)C(Cl)C3)CCC2NCN1 with IC50=0.795943 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na910

b:26.1
occ:1.00
 O A:TYR669 2.3 26.4 1.0
O A:ASP672 2.3 26.3 1.0
O A:MET675 2.3 23.9 1.0
O A:HOH1282 2.4 28.5 1.0
O A:HOH1364 2.6 45.6 1.0
O A:HOH1412 2.9 43.4 1.0
C A:MET675 3.5 23.2 1.0
C A:TYR669 3.5 28.2 1.0
C A:ASP672 3.5 27.2 1.0
N A:MET675 4.1 25.4 1.0
O A:LYS670 4.2 35.2 1.0
CA A:TYR669 4.2 24.6 1.0
CA A:LYS673 4.3 31.9 1.0
N A:SER676 4.3 20.4 1.0
N A:LYS673 4.3 26.4 1.0
CA A:MET675 4.4 24.0 1.0
CA A:ASP672 4.4 28.0 1.0
CA A:SER676 4.4 21.2 1.0
C A:LYS673 4.4 29.8 1.0
N A:ASP672 4.5 27.0 1.0
N A:LYS670 4.5 28.8 1.0
C A:LYS670 4.6 31.9 1.0
O A:LYS673 4.6 31.1 1.0
CB A:TYR669 4.6 23.3 1.0
O A:HOH1430 4.6 42.8 1.0
CA A:LYS670 4.6 32.8 1.0
CB A:ASP672 4.7 29.7 1.0
N A:GLN674 4.9 26.7 1.0
CB A:SER676 5.0 21.0 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 23:09:23 2025

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