Sodium in PDB 2vwm: Aminopyrrolidine Factor Xa Inhibitor

All present enzymatic activity of Aminopyrrolidine Factor Xa Inhibitor:
3.4.21.6;

The structure of Aminopyrrolidine Factor Xa Inhibitor, PDB code: 2vwm was solved by K.Groebke-Zbinden, D.W.Banner, J.M.Benz, F.Blasco, G.Decoret, J.Himber, B.Kuhn, N.Panday, F.Ricklin, P.Risch, D.Schlatter, M.Stahl, R.Unger, W.Haap, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.74 / 1.96
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.930, 77.110, 74.870, 90.00, 92.07, 90.00
R / Rfree (%)	20 / 27.3

The structure of Aminopyrrolidine Factor Xa Inhibitor also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Aminopyrrolidine Factor Xa Inhibitor (pdb code 2vwm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Aminopyrrolidine Factor Xa Inhibitor, PDB code: 2vwm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Aminopyrrolidine Factor Xa Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Aminopyrrolidine Factor Xa Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1245 b:28.6 occ:1.00 O A:ARG222 2.2 32.0 1.0 O A:TYR185 2.2 26.0 1.0 O A:LYS224 2.3 27.0 1.0 O A:HOH2219 2.4 27.8 1.0 O A:ASP185A 2.6 28.8 1.0 O A:HOH2224 2.9 29.5 1.0 C A:ARG222 3.4 33.1 1.0 C A:ASP185A 3.4 28.8 1.0 C A:LYS224 3.4 26.1 1.0 C A:TYR185 3.5 25.8 1.0 N A:LYS224 3.8 27.5 1.0 C A:ALA221 3.9 32.1 1.0 CA A:ASP185A 4.0 28.0 1.0 N A:ARG222 4.0 32.6 1.0 O A:ALA221 4.0 31.8 1.0 N A:ASP185A 4.2 26.8 1.0 CA A:LYS224 4.2 26.9 1.0 CA A:LYS223 4.2 33.7 1.0 N A:GLY223A 4.2 32.4 1.0 N A:LYS223 4.2 33.7 1.0 O A:HOH2198 4.3 31.9 1.0 CA A:ARG222 4.3 33.4 1.0 N A:THR185B 4.4 30.0 1.0 C A:LYS223 4.4 33.1 1.0 CA A:ALA221 4.4 31.5 1.0 N A:TYR225 4.5 24.8 1.0 CA A:TYR185 4.6 24.8 1.0 O A:LYS186 4.7 31.4 1.0 CA A:TYR225 4.7 23.7 1.0 CA A:THR185B 4.7 31.5 1.0 CB A:LYS224 4.8 26.7 1.0 C A:GLY223A 4.8 29.3 1.0 N A:TYR185 4.8 23.6 1.0 CB A:TYR185 5.0 24.5 1.0 CD1 A:TYR225 5.0 21.9 1.0 CA A:GLY223A 5.0 30.4 1.0

Sodium binding site 2 out of 2 in the Aminopyrrolidine Factor Xa Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Aminopyrrolidine Factor Xa Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1245 b:36.4 occ:1.00 O B:LYS224 2.2 34.5 1.0 O B:ARG222 2.2 38.6 1.0 O B:HOH2189 2.4 33.6 1.0 O B:HOH2161 2.4 37.0 1.0 O B:TYR185 2.4 31.2 1.0 O B:ASP185A 3.0 35.2 1.0 C B:ARG222 3.4 39.0 1.0 C B:LYS224 3.4 34.2 1.0 C B:TYR185 3.6 31.6 1.0 C B:ASP185A 3.7 35.2 1.0 N B:LYS224 3.8 36.2 1.0 C B:ALA221 3.8 37.9 1.0 O B:ALA221 3.9 37.7 1.0 N B:ARG222 4.0 38.2 1.0 CA B:ASP185A 4.1 34.8 1.0 CA B:LYS224 4.1 35.2 1.0 N B:GLY223A 4.2 38.4 1.0 N B:LYS223 4.2 38.7 1.0 CA B:LYS223 4.2 39.3 1.0 O B:HOH2158 4.2 23.0 1.0 N B:ASP185A 4.3 33.8 1.0 CA B:ARG222 4.3 38.7 1.0 CA B:ALA221 4.3 37.7 1.0 C B:LYS223 4.4 38.6 1.0 N B:TYR225 4.5 32.1 1.0 N B:THR185B 4.5 36.6 1.0 O B:LYS186 4.6 37.8 1.0 CB B:LYS224 4.6 35.9 1.0 CA B:TYR225 4.7 30.1 1.0 CA B:TYR185 4.7 31.5 1.0 C B:GLY223A 4.8 37.0 1.0 CA B:THR185B 4.9 37.7 1.0 N B:TYR185 4.9 29.6 1.0

K.G.Zbinden, L.Anselm, D.W.Banner, J.M.Benz, F.Blasco, G.Decoret, J.Himber, B.Kuhn, N.Panday, F.Ricklin, P.Risch, D.Schlatter, M.Stahl, S.Thomi, R.Unger, W.Haap. Design of Novel Aminopyrrolidine Factor Xa Inhibitors From A Screening Hit. Eur.J.Med.Chem. V. 44 2787 2009.
ISSN: ISSN 0223-5234
PubMed: 19200624
DOI: 10.1016/J.EJMECH.2008.12.025