Sodium in PDB 5m0m: 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: 5m0m 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)	75.27 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.995, 89.173, 77.289, 90.00, 103.12, 90.00
R / Rfree (%)	20.1 / 24.9

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)	12 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 5m0m). 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: 5m0m:
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:Na926 b:60.5 occ:1.00 O A:HOH1045 2.3 52.6 1.0 O A:MET675 2.6 40.4 1.0 O A:HOH1086 2.7 42.6 1.0 O A:ASP672 2.7 43.3 1.0 O A:TYR669 2.8 43.6 1.0 C A:MET675 3.6 39.1 1.0 C A:ASP672 3.9 44.5 1.0 C A:TYR669 3.9 43.8 1.0 O A:LYS673 4.0 47.5 1.0 N A:SER676 4.3 37.3 1.0 N A:MET675 4.3 41.5 1.0 CA A:SER676 4.3 36.8 1.0 C A:LYS673 4.3 46.6 1.0 CA A:MET675 4.5 39.5 1.0 CA A:LYS673 4.5 47.1 1.0 N A:LYS673 4.7 45.8 1.0 N A:LYS670 4.8 45.9 1.0 CA A:TYR669 4.8 42.4 1.0 CB A:SER676 4.8 37.0 1.0 O A:LYS670 4.8 46.4 1.0 CA A:LYS670 4.9 46.8 1.0 CA A:ASP672 5.0 44.0 1.0 C A:GLN674 5.0 43.5 1.0 CB A:TYR669 5.0 41.8 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:Na927 b:53.8 occ:1.00 O A:HOH1082 2.3 39.3 1.0 O A:HOH1060 2.4 38.4 1.0 OG A:SER807 2.5 37.5 1.0 O A:SER804 2.7 35.3 1.0 O A:ASN801 2.8 32.7 1.0 C A:ASN801 3.6 32.2 1.0 CB A:SER807 3.7 37.4 1.0 C A:SER804 3.8 34.2 1.0 CA A:ASP802 3.9 32.6 1.0 N A:ASP802 4.1 32.3 1.0 N A:SER807 4.3 38.2 1.0 OD1 A:ASP802 4.3 34.3 1.0 CA A:CYS805 4.4 36.3 1.0 O A:ASP802 4.5 32.0 1.0 C A:ASP802 4.5 31.9 1.0 CA A:SER807 4.5 38.5 1.0 N A:CYS805 4.6 34.9 1.0 C A:CYS805 4.6 37.1 1.0 CA A:ASN801 4.7 32.0 1.0 CB A:ASN801 4.7 32.6 1.0 O A:CYS805 4.8 38.0 1.0 CA A:SER804 4.8 32.6 1.0 N A:SER804 4.8 31.7 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