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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;

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;

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

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:
probe atom residue distance (Å) B Occ
H:Na302

b:15.2
occ:1.00
O H:THR172 2.3 16.3 1.0
O H:LYS169 2.4 15.4 1.0
O H:HOH540 2.4 21.2 1.0
O H:HOH462 2.7 22.9 1.0
HA H:ASP170 3.2 18.1 1.0
C H:LYS169 3.4 14.7 1.0
H H:THR172 3.5 18.9 1.0
C H:THR172 3.6 16.4 1.0
HA H:ARG173 3.7 20.4 1.0
CA H:ASP170 4.0 15.0 1.0
N H:ASP170 4.1 14.7 1.0
HG23 H:THR172 4.1 20.3 1.0
HB3 H:LYS169 4.2 19.5 1.0
N H:THR172 4.3 15.8 1.0
C H:ASP170 4.4 15.2 1.0
CA H:ARG173 4.4 17.0 1.0
N H:ARG173 4.4 16.5 1.0
HA H:LYS169 4.5 16.6 1.0
CA H:LYS169 4.5 13.9 1.0
CA H:THR172 4.5 16.7 1.0
OD1 H:ASP170 4.6 19.1 1.0
HG22 H:THR172 4.6 20.3 1.0
O H:ASP170 4.8 16.0 1.0
CG2 H:THR172 4.8 16.9 1.0
CB H:LYS169 4.8 16.2 1.0
N H:SER171 4.9 15.9 1.0
H H:SER171 4.9 19.1 1.0
C H:ARG173 5.0 17.9 1.0
H H:ASP170 5.0 17.6 1.0

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

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:
probe atom residue distance (Å) B Occ
H:Na303

b:18.3
occ:1.00
O H:ARG221A 2.3 19.4 1.0
O H:HOH494 2.4 19.5 1.0
O H:HOH560 2.4 18.0 1.0
O H:LYS224 2.4 16.9 1.0
O H:HOH472 2.5 17.2 1.0
O H:HOH490 2.7 19.6 1.0
H H:LYS224 3.3 20.7 1.0
C H:ARG221A 3.4 19.3 1.0
C H:LYS224 3.4 16.3 1.0
HA H:ASP221 3.7 22.3 1.0
HA H:ASP222 3.8 25.7 1.0
O H:HOH506 3.8 17.5 1.0
HB2 H:LYS224 3.9 20.9 1.0
N H:LYS224 3.9 17.2 1.0
N H:ARG221A 3.9 19.3 1.0
H H:GLY223 3.9 25.1 1.0
HA H:TYR225 3.9 17.8 1.0
H H:ARG221A 4.0 23.1 1.0
O H:HOH470 4.0 23.1 1.0
C H:ASP221 4.0 18.8 1.0
O H:TYR184A 4.1 18.9 1.0
CA H:LYS224 4.1 16.9 1.0
N H:ASP222 4.2 21.1 1.0
CA H:ARG221A 4.2 20.0 1.0
O H:HOH480 4.2 17.5 1.0
N H:GLY223 4.2 20.9 1.0
CA H:ASP222 4.3 21.4 1.0
CA H:ASP221 4.4 18.6 1.0
N H:TYR225 4.4 15.9 1.0
O H:ASP221 4.5 21.2 1.0
CB H:LYS224 4.5 17.5 1.0
C H:ASP222 4.5 21.2 1.0
CA H:TYR225 4.6 14.9 1.0
OD1 H:ASP221 4.7 20.1 1.0
C H:GLY223 4.8 18.6 1.0
HB2 H:ARG221A 4.8 24.5 1.0
HA H:ARG221A 4.9 24.0 1.0
H H:ASP221 5.0 21.8 1.0
O H:HOH465 5.0 19.6 1.0
H H:ASP222 5.0 25.3 1.0
HA3 H:GLY184 5.0 17.1 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: Tue Dec 15 12:17:01 2020

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