Sodium in PDB 5jzy: Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (4-Carbamimidoylbenzyl)Pyrrolidine-2-Carboxamide

All present enzymatic activity of Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (4-Carbamimidoylbenzyl)Pyrrolidine-2-Carboxamide:
3.4.21.5;

The structure of Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (4-Carbamimidoylbenzyl)Pyrrolidine-2-Carboxamide, PDB code: 5jzy was solved by A.Sandner, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.56 / 1.27
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	69.920, 71.509, 72.295, 90.00, 100.50, 90.00
R / Rfree (%)	12 / 14.2

The binding sites of Sodium atom in the Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (4-Carbamimidoylbenzyl)Pyrrolidine-2-Carboxamide (pdb code 5jzy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (4-Carbamimidoylbenzyl)Pyrrolidine-2-Carboxamide, PDB code: 5jzy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (4-Carbamimidoylbenzyl)Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (4-Carbamimidoylbenzyl)Pyrrolidine-2-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ H:Na305 b:15.2 occ:1.00 O H:ARG221A 2.3 16.0 1.0 O H:HOH472 2.4 16.0 1.0 O H:HOH601 2.4 15.9 1.0 O H:LYS224 2.4 14.2 1.0 O H:HOH498 2.5 13.8 1.0 O H:HOH507 2.6 17.7 1.0 H H:LYS224 3.3 17.2 1.0 C H:ARG221A 3.4 16.7 1.0 C H:LYS224 3.5 13.0 1.0 HA H:ASP222 3.7 22.2 1.0 HA H:ASP221 3.7 18.0 1.0 H H:GLY223 3.8 19.9 1.0 N H:LYS224 3.8 14.3 1.0 O H:HOH525 3.9 15.0 1.0 O H:HOH468 3.9 19.8 1.0 HB2 H:LYS224 3.9 17.7 1.0 N H:ARG221A 4.0 15.3 1.0 O H:TYR184A 4.1 15.8 1.0 HA H:TYR225 4.1 14.8 1.0 C H:ASP221 4.1 15.8 1.0 H H:ARG221A 4.1 18.3 1.0 N H:GLY223 4.2 16.6 1.0 N H:ASP222 4.2 18.4 1.0 CA H:LYS224 4.2 13.7 1.0 CA H:ASP222 4.2 18.5 1.0 O H:HOH476 4.2 14.9 1.0 CA H:ARG221A 4.3 16.0 1.0 CA H:ASP221 4.4 15.0 1.0 C H:ASP222 4.4 17.4 1.0 O H:ASP221 4.5 17.4 1.0 N H:TYR225 4.5 12.3 1.0 OD2 H:ASP221 4.6 16.2 1.0 CB H:LYS224 4.6 14.8 1.0 O H:HOH447 4.6 17.2 1.0 CA H:TYR225 4.8 12.3 1.0 C H:GLY223 4.8 15.3 1.0 HB2 H:ARG221A 4.9 20.6 1.0 H H:ASP222 5.0 22.1 1.0 HA3 H:GLY184 5.0 14.1 1.0 HA H:ARG221A 5.0 19.2 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (4-Carbamimidoylbenzyl)Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (4-Carbamimidoylbenzyl)Pyrrolidine-2-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ H:Na306 b:12.3 occ:1.00 O H:THR172 2.3 12.7 1.0 O H:LYS169 2.4 12.9 1.0 O H:HOH615 2.4 15.8 1.0 O H:HOH575 2.4 19.4 1.0 O H:HOH499 2.6 17.1 1.0 HA H:ASP170 3.2 14.9 1.0 C H:LYS169 3.5 12.7 1.0 H H:THR172 3.5 14.5 1.0 C H:THR172 3.6 11.1 1.0 HA H:ARG173 3.7 15.4 1.0 CA H:ASP170 4.0 12.4 1.0 N H:ASP170 4.1 12.1 1.0 N H:THR172 4.2 12.1 1.0 HG23 H:THR172 4.3 15.6 1.0 C H:ASP170 4.4 12.9 1.0 N H:ARG173 4.4 12.3 1.0 CA H:ARG173 4.4 12.8 1.0 HA H:LYS169 4.5 15.0 1.0 CA H:THR172 4.5 12.2 1.0 CA H:LYS169 4.5 12.5 1.0 O H:HOH466 4.6 39.3 1.0 OD1 H:ASP170 4.6 17.0 1.0 HG22 H:THR172 4.6 15.6 1.0 O H:ASP170 4.8 12.8 1.0 N H:SER171 4.8 12.2 1.0 H H:SER171 4.9 14.6 1.0 CG2 H:THR172 4.9 13.0 1.0 CB H:LYS169 4.9 14.5 1.0 C H:ARG173 5.0 13.5 1.0 H H:ASP170 5.0 14.5 1.0

A.Sandner, T.Hufner-Wulsdorf, A.Heine, T.Steinmetzer, G.Klebe. Strategies For Late-Stage Optimization: Profiling Thermodynamics By Preorganization and Salt Bridge Shielding. J.Med.Chem. V. 62 9753 2019.
ISSN: ISSN 0022-2623
PubMed: 31633354
DOI: 10.1021/ACS.JMEDCHEM.9B01196