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Sodium in PDB 5lce: Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (5-Chloro-2-(Hydroxymethyl)Benzy L)Pyrrolidine-2-Carboxamide

Enzymatic activity of Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (5-Chloro-2-(Hydroxymethyl)Benzy L)Pyrrolidine-2-Carboxamide

All present enzymatic activity of Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (5-Chloro-2-(Hydroxymethyl)Benzy L)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- (5-Chloro-2-(Hydroxymethyl)Benzy L)Pyrrolidine-2-Carboxamide, PDB code: 5lce 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) 43.39 / 1.39
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 69.873, 71.200, 72.636, 90.00, 100.44, 90.00
R / Rfree (%) 14 / 16.8

Other elements in 5lce:

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

Sodium binding site 1 out of 2 in 5lce

Go back to Sodium Binding Sites List in 5lce
Sodium binding site 1 out of 2 in the Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (5-Chloro-2-(Hydroxymethyl)Benzy L)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- (5-Chloro-2-(Hydroxymethyl)Benzy L)Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na305

b:18.7
occ:1.00
 O H:ARG221A 2.3 19.0 1.0
O H:LYS224 2.4 17.1 0.5
O H:HOH580 2.4 20.8 1.0
O H:HOH468 2.4 20.2 1.0
O H:HOH496 2.5 16.2 1.0
O H:LYS224 2.5 17.0 0.5
O H:HOH497 2.7 20.4 1.0
C H:ARG221A 3.4 19.2 1.0
C H:LYS224 3.4 15.8 0.5
C H:LYS224 3.5 15.8 0.5
O H:HOH520 3.8 18.9 1.0
N H:LYS224 3.9 17.0 0.5
N H:ARG221A 3.9 18.6 1.0
N H:LYS224 3.9 17.2 0.5
O H:HOH509 3.9 22.9 1.0
C H:ASP221 4.1 19.9 1.0
O H:TYR184A 4.1 17.9 1.0
CA H:LYS224 4.2 16.6 0.5
CA H:LYS224 4.2 16.1 0.5
O H:HOH491 4.2 17.6 1.0
N H:ASP222 4.2 21.4 1.0
CA H:ARG221A 4.2 19.8 1.0
CA H:ASP222 4.3 22.1 1.0
N H:GLY223 4.3 20.9 1.0
CA H:ASP221 4.3 19.1 1.0
N H:TYR225 4.5 15.3 1.0
CB H:LYS224 4.5 17.2 0.5
CB H:LYS224 4.5 16.3 0.5
C H:ASP222 4.5 21.9 1.0
O H:ASP221 4.6 22.5 1.0
OD1 H:ASP221 4.6 19.8 1.0
CA H:TYR225 4.8 14.8 1.0
C H:GLY223 4.9 17.8 1.0
O H:HOH566 5.0 20.0 1.0

Sodium binding site 2 out of 2 in 5lce

Go back to Sodium Binding Sites List in 5lce
Sodium binding site 2 out of 2 in the Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (5-Chloro-2-(Hydroxymethyl)Benzy L)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- (5-Chloro-2-(Hydroxymethyl)Benzy L)Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na306

b:15.0
occ:1.00
 O H:THR172 2.3 14.8 1.0
O H:HOH478 2.3 31.0 1.0
O H:LYS169 2.4 15.2 0.3
O H:HOH604 2.4 19.4 1.0
O H:LYS169 2.4 16.1 0.7
O H:HOH482 2.7 22.0 1.0
C H:LYS169 3.5 14.4 0.3
C H:LYS169 3.5 14.7 0.7
C H:THR172 3.6 14.7 1.0
CA H:ASP170 4.1 14.1 1.0
CG H:LYS169 4.2 21.0 0.7
N H:ASP170 4.2 13.9 1.0
N H:THR172 4.3 14.4 1.0
CG H:LYS169 4.3 18.0 0.3
C H:ASP170 4.4 14.0 1.0
CA H:ARG173 4.4 14.9 1.0
N H:ARG173 4.4 14.6 1.0
NZ H:LYS169 4.5 22.6 0.3
CA H:LYS169 4.5 14.8 0.7
CA H:LYS169 4.5 14.5 0.3
CA H:THR172 4.5 15.3 1.0
O H:HOH483 4.6 36.6 1.0
OD1 H:ASP170 4.8 20.5 1.0
O H:ASP170 4.8 15.6 1.0
N H:SER171 4.9 13.9 1.0
CG2 H:THR172 4.9 16.4 1.0
CB H:LYS169 4.9 16.9 0.7
CB H:LYS169 4.9 15.6 0.3

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 22:19:56 2024

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