Atomistry » Sodium » PDB 7f5i-7g32 » 7g2e
Atomistry »
  Sodium »
    PDB 7f5i-7g32 »
      7g2e »

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

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy