Sodium in PDB 2vwn: 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: 2vwn 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)	74.54 / 1.61
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	105.540, 105.540, 49.790, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 22.8

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

Fluorine	(F)	1 atom
Calcium	(Ca)	1 atom
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Aminopyrrolidine Factor Xa Inhibitor (pdb code 2vwn). 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: 2vwn:
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:Na1247 b:21.1 occ:1.00 O A:LYS224 2.3 19.0 0.5 O A:LYS224 2.3 19.1 0.5 O A:TYR185 2.3 21.2 1.0 O A:ARG222 2.3 21.3 1.0 O A:ASP185A 2.3 22.4 1.0 O A:HOH2184 2.3 25.1 1.0 O A:HOH2205 2.8 23.2 1.0 C A:ASP185A 3.2 23.4 1.0 C A:ARG222 3.4 21.3 1.0 C A:LYS224 3.4 18.1 0.5 C A:LYS224 3.4 18.0 0.5 C A:TYR185 3.4 20.9 1.0 N A:LYS224 3.7 18.9 0.5 N A:LYS224 3.7 19.0 0.5 CA A:ASP185A 3.8 22.8 1.0 N A:ASP185A 4.1 21.6 1.0 CA A:LYS224 4.1 18.7 0.5 N A:ARG222 4.1 22.0 1.0 CA A:LYS224 4.1 18.5 0.5 C A:ALA221 4.1 22.4 1.0 N A:THR185B 4.1 23.8 1.0 N A:GLY223A 4.1 21.5 1.0 N A:LYS223 4.2 21.9 1.0 CA A:LYS223 4.2 22.8 1.0 O A:ALA221 4.4 23.6 1.0 CA A:ARG222 4.4 21.3 1.0 C A:LYS223 4.4 21.9 1.0 O A:HOH2188 4.5 21.9 1.0 N A:TYR225 4.5 17.5 1.0 CA A:ALA221 4.5 22.0 1.0 CA A:THR185B 4.5 25.1 1.0 CB A:LYS224 4.6 19.0 0.5 CA A:TYR185 4.7 20.3 1.0 CB A:LYS224 4.7 18.7 0.5 O A:LYS186 4.7 24.5 1.0 C A:GLY223A 4.7 19.9 1.0 CA A:TYR225 4.8 17.4 1.0 N A:TYR185 4.9 19.2 1.0 CA A:GLY223A 4.9 20.9 1.0 C A:THR185B 5.0 25.1 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 A:Na1250 b:67.2 occ:1.00 O A:HOH2045 2.1 47.5 1.0 O A:HOH2121 2.2 27.5 1.0 O A:HOH2148 2.3 47.1 1.0 O A:HOH2119 2.4 73.4 1.0 O A:HOH2046 2.4 43.2 1.0 O A:HOH2057 4.0 62.1 1.0 O A:THR132 4.2 24.5 1.0 O A:HOH2151 4.3 48.0 1.0 O A:GLN133 4.3 24.0 1.0 O A:MET131B 4.4 24.6 1.0 CA A:THR132 4.5 24.4 1.0 C A:THR132 4.5 24.7 1.0 O A:HOH2123 4.7 27.0 1.0 CB A:TYR162 4.8 18.0 1.0 O A:HOH2152 5.0 44.5 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