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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
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