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Sodium in PDB 5lpd: Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (2-(Aminomethyl)-5-Chlorobenzyl) Pyrrolidine-2-Carboxamide

Enzymatic activity of Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (2-(Aminomethyl)-5-Chlorobenzyl) Pyrrolidine-2-Carboxamide

All present enzymatic activity of Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (2-(Aminomethyl)-5-Chlorobenzyl) Pyrrolidine-2-Carboxamide:
3.4.21.5;

Protein crystallography data

The structure of Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (2-(Aminomethyl)-5-Chlorobenzyl) Pyrrolidine-2-Carboxamide, PDB code: 5lpd 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) 49.46 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.124, 70.994, 72.830, 90.00, 100.50, 90.00
R / Rfree (%) 14.9 / 17

Other elements in 5lpd:

The structure of Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (2-(Aminomethyl)-5-Chlorobenzyl) 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)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (2-(Aminomethyl)-5-Chlorobenzyl) Pyrrolidine-2-Carboxamide (pdb code 5lpd). 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- (2-(Aminomethyl)-5-Chlorobenzyl) Pyrrolidine-2-Carboxamide, PDB code: 5lpd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5lpd

Go back to Sodium Binding Sites List in 5lpd
Sodium binding site 1 out of 2 in the Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (2-(Aminomethyl)-5-Chlorobenzyl) 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- (2-(Aminomethyl)-5-Chlorobenzyl) Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na302

b:16.6
occ:1.00
 O H:LYS169 2.3 17.1 0.4
O H:THR172 2.3 16.7 1.0
O H:HOH567 2.5 27.1 1.0
O H:LYS169 2.5 16.0 0.6
O H:HOH506 2.6 24.7 1.0
HA H:ASP170 3.3 20.9 1.0
C H:LYS169 3.5 15.9 0.4
C H:LYS169 3.5 15.8 0.6
H H:THR172 3.5 19.5 1.0
C H:THR172 3.6 15.5 1.0
HA H:ARG173 3.6 19.5 1.0
CA H:ASP170 4.0 17.4 1.0
CG H:LYS169 4.1 16.2 0.6
HG23 H:THR172 4.2 19.6 1.0
N H:ASP170 4.2 16.8 1.0
HB3 H:LYS169 4.3 17.5 0.4
N H:THR172 4.3 16.3 1.0
CA H:ARG173 4.4 16.2 1.0
C H:ASP170 4.4 16.9 1.0
N H:ARG173 4.4 14.9 1.0
HA H:LYS169 4.5 17.5 0.4
HA H:LYS169 4.5 17.5 0.6
O H:HOH446 4.5 43.0 1.0
CA H:LYS169 4.5 14.6 0.4
CA H:LYS169 4.5 14.6 0.6
HG22 H:THR172 4.5 19.6 1.0
CA H:THR172 4.6 15.7 1.0
OD1 H:ASP170 4.7 20.1 1.0
O H:ASP170 4.7 16.4 1.0
CG2 H:THR172 4.8 16.3 1.0
CB H:LYS169 4.9 14.6 0.6
N H:SER171 4.9 16.0 1.0
CB H:LYS169 4.9 14.6 0.4
H H:SER171 5.0 19.2 1.0
C H:ARG173 5.0 17.0 1.0

Sodium binding site 2 out of 2 in 5lpd

Go back to Sodium Binding Sites List in 5lpd
Sodium binding site 2 out of 2 in the Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (2-(Aminomethyl)-5-Chlorobenzyl) 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- (2-(Aminomethyl)-5-Chlorobenzyl) Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na303

b:17.5
occ:1.00
 O H:HOH578 2.3 17.5 1.0
O H:ARG221A 2.3 19.0 1.0
O H:HOH469 2.4 18.1 1.0
O H:LYS224 2.4 15.4 1.0
O H:HOH498 2.5 16.3 1.0
O H:HOH523 2.6 19.0 1.0
H H:LYS224 3.3 19.8 1.0
C H:ARG221A 3.4 19.2 1.0
C H:LYS224 3.4 15.6 1.0
HA H:ASP221 3.7 20.6 1.0
HA H:ASP222 3.8 22.5 1.0
HB2 H:LYS224 3.8 18.8 1.0
N H:LYS224 3.9 16.5 1.0
O H:HOH537 3.9 16.2 1.0
N H:ARG221A 3.9 18.7 1.0
H H:GLY223 3.9 24.9 1.0
HA H:TYR225 3.9 17.5 1.0
H H:ARG221A 4.0 22.4 1.0
O H:HOH467 4.0 20.2 1.0
C H:ASP221 4.1 18.4 1.0
CA H:LYS224 4.1 15.7 1.0
O H:TYR184A 4.1 17.8 1.0
N H:ASP222 4.2 18.8 1.0
CA H:ARG221A 4.3 19.3 1.0
O H:HOH481 4.3 16.9 1.0
N H:GLY223 4.3 20.8 1.0
CA H:ASP222 4.3 18.7 1.0
N H:TYR225 4.4 15.4 1.0
CA H:ASP221 4.4 17.1 1.0
CB H:LYS224 4.4 15.7 1.0
O H:ASP221 4.5 19.6 1.0
C H:ASP222 4.5 19.6 1.0
CA H:TYR225 4.6 14.6 1.0
OD1 H:ASP221 4.6 17.2 1.0
HB2 H:ARG221A 4.8 22.6 1.0
C H:GLY223 4.8 18.8 1.0
HB3 H:LYS224 4.9 18.8 1.0
O H:HOH475 4.9 18.5 1.0
HA H:ARG221A 5.0 23.1 1.0
HB2 H:ASP189 5.0 17.3 1.0
H H:ASP221 5.0 20.0 1.0
HA3 H:GLY184 5.0 17.4 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 22:22:40 2024

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