Sodium in PDB 4lxb: Crystal Structure Analysis of Thrombin in Complex with Compound D58

All present enzymatic activity of Crystal Structure Analysis of Thrombin in Complex with Compound D58:
3.4.21.5;

The structure of Crystal Structure Analysis of Thrombin in Complex with Compound D58, PDB code: 4lxb was solved by C.Stehlin-Gaon, Z.Bocskei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.68 / 1.61
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.623, 71.274, 72.858, 90.00, 100.84, 90.00
R / Rfree (%)	19 / 22.8

The structure of Crystal Structure Analysis of Thrombin in Complex with Compound D58 also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure Analysis of Thrombin in Complex with Compound D58 (pdb code 4lxb). 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 Analysis of Thrombin in Complex with Compound D58, PDB code: 4lxb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure Analysis of Thrombin in Complex with Compound D58


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Analysis of Thrombin in Complex with Compound D58 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:25.7 occ:1.00 O H:HOH566 2.3 25.2 1.0 O H:HOH618 2.3 25.2 1.0 O H:ARG221A 2.4 28.1 1.0 O H:LYS224 2.4 25.0 1.0 O H:HOH433 2.5 22.8 1.0 O H:HOH423 2.8 25.3 1.0 C H:ARG221A 3.4 29.4 1.0 C H:LYS224 3.5 25.4 1.0 N H:LYS224 3.8 25.2 1.0 N H:ARG221A 3.9 26.1 1.0 O H:HOH419 3.9 22.9 1.0 O H:HOH410 4.0 27.8 1.0 C H:ASP221 4.0 29.2 1.0 CA H:LYS224 4.2 22.8 1.0 O H:TYR184A 4.2 27.3 1.0 N H:ASP222 4.2 28.4 1.0 O H:HOH411 4.2 23.8 1.0 N H:GLY223 4.3 28.9 1.0 CA H:ARG221A 4.3 27.3 1.0 CA H:ASP222 4.3 29.5 1.0 CA H:ASP221 4.3 24.8 1.0 N H:TYR225 4.4 23.5 1.0 CB H:LYS224 4.5 23.8 1.0 O H:ASP221 4.5 30.0 1.0 C H:ASP222 4.5 32.9 1.0 OD1 H:ASP221 4.6 26.9 1.0 CA H:TYR225 4.7 22.6 1.0 C H:GLY223 4.9 29.8 1.0 O H:HOH563 5.0 23.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure Analysis of Thrombin in Complex with Compound D58


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure Analysis of Thrombin in Complex with Compound D58 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na303 b:23.8 occ:1.00 O H:HOH402 2.3 25.1 1.0 O H:THR172 2.4 25.5 1.0 O H:LYS169 2.4 26.4 1.0 O H:HOH443 2.5 29.2 1.0 O H:HOH456 2.6 28.7 1.0 C H:LYS169 3.5 26.1 1.0 C H:THR172 3.6 26.4 1.0 CA H:ASP170 4.1 23.6 1.0 N H:ASP170 4.2 22.8 1.0 N H:THR172 4.3 22.4 1.0 O H:HOH524 4.4 61.3 1.0 CA H:ARG173 4.4 24.4 1.0 N H:ARG173 4.5 24.2 1.0 C H:ASP170 4.5 26.3 1.0 CA H:LYS169 4.5 21.2 1.0 CA H:THR172 4.6 22.3 1.0 O H:HOH637 4.6 46.7 1.0 OD1 H:ASP170 4.7 31.0 1.0 CG2 H:THR172 4.8 24.6 1.0 O H:ASP170 4.8 26.3 1.0 O H:HOH686 4.8 50.0 1.0 CB H:LYS169 4.9 23.3 1.0 C H:ARG173 4.9 27.4 1.0 N H:SER171 4.9 22.8 1.0 O H:ILE174 5.0 25.3 1.0

J.Meneyrol, M.Follmann, G.Lassalle, V.Wehner, G.Barre, T.Rousseaux, J.M.Altenburger, F.Petit, Z.Bocskei, H.Schreuder, N.Alet, J.P.Herault, L.Millet, F.Dol, P.Florian, P.Schaeffer, F.Sadoun, S.Klieber, C.Briot, F.Bono, J.M.Herbert. 5-Chlorothiophene-2-Carboxylic Acid [(S)-2-[2-Methyl-3-(2-Oxopyrrolidin-1-Yl) Benzenesulfonylamino]-3-(4-Methylpiperazin-1-Yl)-3- Oxopropyl]Amide (SAR107375), A Selective and Potent Orally Active Dual Thrombin and Factor Xa Inhibitor. J.Med.Chem. V. 56 9441 2013.
ISSN: ISSN 0022-2623
PubMed: 24175584
DOI: 10.1021/JM4005835