Sodium »
PDB 6g3r-6gn7 »
6gbw »
Sodium in PDB 6gbw: Thrombin in Complex with MI2100 ((S)-N-(2-(Aminomethyl)-5- Chlorobenzyl)-1-((Benzylsulfonyl)-L-Arginyl)Pyrrolidine-2- Carboxamide)
Enzymatic activity of Thrombin in Complex with MI2100 ((S)-N-(2-(Aminomethyl)-5- Chlorobenzyl)-1-((Benzylsulfonyl)-L-Arginyl)Pyrrolidine-2- Carboxamide)
All present enzymatic activity of Thrombin in Complex with MI2100 ((S)-N-(2-(Aminomethyl)-5- Chlorobenzyl)-1-((Benzylsulfonyl)-L-Arginyl)Pyrrolidine-2- Carboxamide):
3.4.21.5;
3.4.21.5;
Protein crystallography data
The structure of Thrombin in Complex with MI2100 ((S)-N-(2-(Aminomethyl)-5- Chlorobenzyl)-1-((Benzylsulfonyl)-L-Arginyl)Pyrrolidine-2- Carboxamide), PDB code: 6gbw
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) | 21.78 / 1.45 |
| Space group | C 1 2 1 |
| Cell size a, b, c (Å), α, β, γ (°) | 69.840, 71.119, 72.858, 90.00, 100.58, 90.00 |
| R / Rfree (%) | 13.2 / 16.5 |
Other elements in 6gbw:
The structure of Thrombin in Complex with MI2100 ((S)-N-(2-(Aminomethyl)-5- Chlorobenzyl)-1-((Benzylsulfonyl)-L-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 MI2100 ((S)-N-(2-(Aminomethyl)-5- Chlorobenzyl)-1-((Benzylsulfonyl)-L-Arginyl)Pyrrolidine-2- Carboxamide)
(pdb code 6gbw). 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 MI2100 ((S)-N-(2-(Aminomethyl)-5- Chlorobenzyl)-1-((Benzylsulfonyl)-L-Arginyl)Pyrrolidine-2- Carboxamide), PDB code: 6gbw:
Jump to Sodium binding site number: 1; 2;
In total 2 binding sites of Sodium where determined in the Thrombin in Complex with MI2100 ((S)-N-(2-(Aminomethyl)-5- Chlorobenzyl)-1-((Benzylsulfonyl)-L-Arginyl)Pyrrolidine-2- Carboxamide), PDB code: 6gbw:
Jump to Sodium binding site number: 1; 2;
Sodium binding site 1 out of 2 in 6gbw
Go back to
Sodium Binding Sites List in 6gbw
Sodium binding site 1 out
of 2 in the Thrombin in Complex with MI2100 ((S)-N-(2-(Aminomethyl)-5- Chlorobenzyl)-1-((Benzylsulfonyl)-L-Arginyl)Pyrrolidine-2- Carboxamide)
Mono view
Stereo pair view
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 MI2100 ((S)-N-(2-(Aminomethyl)-5- Chlorobenzyl)-1-((Benzylsulfonyl)-L-Arginyl)Pyrrolidine-2- Carboxamide) within 5.0Å range:
|
Sodium binding site 2 out of 2 in 6gbw
Go back to
Sodium Binding Sites List in 6gbw
Sodium binding site 2 out
of 2 in the Thrombin in Complex with MI2100 ((S)-N-(2-(Aminomethyl)-5- Chlorobenzyl)-1-((Benzylsulfonyl)-L-Arginyl)Pyrrolidine-2- Carboxamide)
Mono view
Stereo pair view
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 MI2100 ((S)-N-(2-(Aminomethyl)-5- Chlorobenzyl)-1-((Benzylsulfonyl)-L-Arginyl)Pyrrolidine-2- Carboxamide) within 5.0Å range:
|
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: Tue Oct 8 08:59:32 2024
ISSN: ISSN 0022-2623
PubMed: 31633354
DOI: 10.1021/ACS.JMEDCHEM.9B01196
Last articles
Zn in 9JPJZn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
