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Sodium in PDB 5jfd: Thrombin in Complex with (S)-N-(2-(Aminomethyl)-5-Chlorobenzyl)-1- ((Benzylsulfonyl)-D-Arginyl)Pyrrolidine-2-Carboxamide

Enzymatic activity of Thrombin in Complex with (S)-N-(2-(Aminomethyl)-5-Chlorobenzyl)-1- ((Benzylsulfonyl)-D-Arginyl)Pyrrolidine-2-Carboxamide

All present enzymatic activity of Thrombin in Complex with (S)-N-(2-(Aminomethyl)-5-Chlorobenzyl)-1- ((Benzylsulfonyl)-D-Arginyl)Pyrrolidine-2-Carboxamide:
3.4.21.5;

Protein crystallography data

The structure of Thrombin in Complex with (S)-N-(2-(Aminomethyl)-5-Chlorobenzyl)-1- ((Benzylsulfonyl)-D-Arginyl)Pyrrolidine-2-Carboxamide, PDB code: 5jfd 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) 43.13 / 1.46
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 69.367, 71.490, 72.135, 90.00, 99.79, 90.00
R / Rfree (%) 13 / 16.3

Other elements in 5jfd:

The structure of Thrombin in Complex with (S)-N-(2-(Aminomethyl)-5-Chlorobenzyl)-1- ((Benzylsulfonyl)-D-Arginyl)Pyrrolidine-2-Carboxamide also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Thrombin in Complex with (S)-N-(2-(Aminomethyl)-5-Chlorobenzyl)-1- ((Benzylsulfonyl)-D-Arginyl)Pyrrolidine-2-Carboxamide (pdb code 5jfd). 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)-N-(2-(Aminomethyl)-5-Chlorobenzyl)-1- ((Benzylsulfonyl)-D-Arginyl)Pyrrolidine-2-Carboxamide, PDB code: 5jfd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5jfd

Go back to Sodium Binding Sites List in 5jfd
Sodium binding site 1 out of 2 in the Thrombin in Complex with (S)-N-(2-(Aminomethyl)-5-Chlorobenzyl)-1- ((Benzylsulfonyl)-D-Arginyl)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)-N-(2-(Aminomethyl)-5-Chlorobenzyl)-1- ((Benzylsulfonyl)-D-Arginyl)Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na303

b:17.0
occ:1.00
 O H:THR172 2.3 17.5 1.0
O H:HOH559 2.4 22.8 1.0
O H:LYS169 2.4 18.0 1.0
O H:HOH477 2.6 27.3 1.0
HA H:ASP170 3.2 20.6 1.0
C H:LYS169 3.5 18.1 1.0
H H:THR172 3.5 19.9 1.0
C H:THR172 3.6 17.4 1.0
HA H:ARG173 3.7 21.6 1.0
CA H:ASP170 4.0 17.2 1.0
HG23 H:THR172 4.1 22.2 1.0
N H:ASP170 4.2 17.2 1.0
HB3 H:LYS169 4.2 24.4 1.0
N H:THR172 4.3 16.6 1.0
C H:ASP170 4.4 17.5 1.0
CA H:ARG173 4.4 18.0 1.0
N H:ARG173 4.4 17.4 1.0
HA H:LYS169 4.5 20.6 1.0
CA H:LYS169 4.5 17.2 1.0
CA H:THR172 4.6 17.2 1.0
OD1 H:ASP170 4.6 20.1 1.0
HG22 H:THR172 4.6 22.2 1.0
O H:HOH625 4.6 47.5 1.0
O H:ASP170 4.8 17.1 1.0
CG2 H:THR172 4.8 18.5 1.0
O H:HOH429 4.8 49.5 1.0
N H:SER171 4.8 17.0 1.0
CB H:LYS169 4.9 20.4 1.0
H H:SER171 4.9 20.4 1.0
C H:ARG173 4.9 19.5 1.0
O H:ILE174 4.9 20.7 1.0
H H:ASP170 5.0 20.7 1.0

Sodium binding site 2 out of 2 in 5jfd

Go back to Sodium Binding Sites List in 5jfd
Sodium binding site 2 out of 2 in the Thrombin in Complex with (S)-N-(2-(Aminomethyl)-5-Chlorobenzyl)-1- ((Benzylsulfonyl)-D-Arginyl)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)-N-(2-(Aminomethyl)-5-Chlorobenzyl)-1- ((Benzylsulfonyl)-D-Arginyl)Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na304

b:19.1
occ:1.00
 O H:HOH587 2.3 18.8 1.0
O H:ARG221A 2.3 19.7 1.0
O H:HOH469 2.3 19.6 1.0
O H:LYS224 2.5 17.9 1.0
O H:HOH496 2.5 17.9 1.0
O H:HOH525 2.6 20.6 1.0
H H:LYS224 3.3 22.9 1.0
C H:ARG221A 3.4 19.7 1.0
C H:LYS224 3.4 17.2 1.0
HA H:ASP221 3.7 22.6 1.0
HB2 H:LYS224 3.7 21.1 1.0
HA H:ASP222 3.8 27.3 1.0
O H:HOH538 3.8 16.3 1.0
N H:LYS224 3.9 19.0 1.0
H H:GLY223 3.9 26.4 1.0
N H:ARG221A 3.9 19.3 1.0
H H:ARG221A 3.9 23.2 1.0
HA H:TYR225 4.0 19.6 1.0
O H:HOH510 4.0 26.1 1.0
C H:ASP221 4.1 19.8 1.0
CA H:LYS224 4.1 18.1 1.0
O H:TYR184A 4.2 19.5 1.0
N H:ASP222 4.2 21.4 1.0
N H:GLY223 4.2 22.0 1.0
CA H:ARG221A 4.3 20.4 1.0
O H:HOH522 4.3 17.9 1.0
CA H:ASP222 4.3 22.8 1.0
CA H:ASP221 4.4 18.9 1.0
N H:TYR225 4.4 16.9 1.0
CB H:LYS224 4.4 17.6 1.0
O H:ASP221 4.5 21.5 1.0
C H:ASP222 4.5 21.9 1.0
OD1 H:ASP221 4.6 20.1 1.0
CA H:TYR225 4.7 16.4 1.0
C H:GLY223 4.8 20.3 1.0
HB2 H:ARG221A 4.9 24.4 1.0
HB3 H:LYS224 4.9 21.1 1.0
HB2 H:ASP189 4.9 19.2 1.0
HA H:ARG221A 5.0 24.5 1.0
HA3 H:GLY184 5.0 18.9 1.0
H H:ASP222 5.0 25.7 1.0
H H:ASP221 5.0 21.3 1.0

Reference:

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
Page generated: Mon Oct 7 21:52:55 2024

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