Sodium in PDB 5m0e: Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors

All present enzymatic activity of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors:
3.1.4.39;

The structure of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors, PDB code: 5m0e was solved by W.-J.Keune, T.Heidebrecht, A.Perrakis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.15 / 1.95
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.618, 61.729, 63.696, 103.43, 98.18, 93.50
R / Rfree (%)	18.1 / 22.3

The structure of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Iodine	(I)	14 atoms
Calcium	(Ca)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors (pdb code 5m0e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors, PDB code: 5m0e:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Na919 b:27.5 occ:1.00 O A:HOH1215 2.3 37.4 1.0 OG A:SER807 2.3 25.5 1.0 O A:SER804 2.4 23.1 1.0 O A:ASN801 2.5 20.7 1.0 O A:HOH1095 2.5 27.2 1.0 O A:HOH1196 2.6 29.7 1.0 C A:ASN801 3.3 21.3 1.0 CB A:SER807 3.4 25.8 1.0 C A:SER804 3.4 23.8 1.0 CA A:ASP802 3.9 21.8 1.0 N A:ASP802 4.0 21.5 1.0 N A:SER807 4.1 26.5 1.0 CB A:ASN801 4.2 22.3 1.0 CA A:CYS805 4.3 27.1 1.0 CA A:SER807 4.3 26.8 1.0 N A:CYS805 4.3 24.9 1.0 O A:HOH1057 4.3 33.7 1.0 C A:ASP802 4.3 20.3 1.0 N A:SER804 4.3 22.0 1.0 O A:ASP802 4.3 19.9 1.0 CA A:SER804 4.4 22.3 1.0 CA A:ASN801 4.4 21.8 1.0 O A:HOH1157 4.4 29.4 1.0 C A:CYS805 4.5 26.9 1.0 O A:CYS805 4.6 27.7 1.0 CB A:SER804 4.6 22.6 1.0 OD1 A:ASP802 4.7 25.2 1.0 C A:SER807 4.9 28.7 1.0

Sodium binding site 2 out of 2 in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Na920 b:35.2 occ:1.00 O A:ASP672 2.3 34.7 1.0 O A:MET675 2.3 28.9 1.0 O A:TYR669 2.3 34.1 1.0 O A:HOH1156 2.5 36.6 1.0 O A:HOH1205 2.7 38.9 1.0 O A:HOH1192 2.7 42.0 1.0 C A:MET675 3.5 28.8 1.0 C A:ASP672 3.5 35.5 1.0 C A:TYR669 3.5 34.5 1.0 N A:MET675 4.1 31.5 1.0 C A:LYS673 4.3 36.1 1.0 O A:LYS673 4.3 35.4 1.0 CA A:LYS673 4.3 37.2 1.0 CA A:TYR669 4.3 33.0 1.0 CA A:MET675 4.3 29.8 1.0 N A:LYS673 4.4 36.0 1.0 N A:SER676 4.4 26.0 1.0 O A:LYS670 4.4 37.8 1.0 N A:LYS670 4.5 36.4 1.0 CA A:ASP672 4.5 35.2 1.0 N A:ASP672 4.5 37.1 1.0 CA A:LYS670 4.6 38.4 1.0 CA A:SER676 4.6 25.8 1.0 C A:LYS670 4.6 38.3 1.0 CB A:ASP672 4.7 34.0 1.0 CB A:TYR669 4.8 31.9 1.0 N A:GLN674 4.8 36.0 1.0 CB A:MET675 5.0 29.1 1.0

W.J.Keune, F.Potjewyd, T.Heidebrecht, F.Salgado-Polo, S.J.Macdonald, L.Chelvarajan, A.Abdel Latif, S.Soman, A.J.Morris, A.J.Watson, C.Jamieson, A.Perrakis. Rational Design of Autotaxin Inhibitors By Structural Evolution of Endogenous Modulators. J. Med. Chem. V. 60 2006 2017.
ISSN: ISSN 1520-4804
PubMed: 28165241
DOI: 10.1021/ACS.JMEDCHEM.6B01743