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Sodium in PDB 4loy: Crystal Structure Analysis of Thrombin in Complex with Compound D57, 5-Chlorothiophene-2-Carboxylic Acid [(S)-2-[2-Methyl-3-(2- Oxopyrrolidin-1-Yl)Benzenesulfonylamino]-3-(4-Methylpiperazin-1- Yl)- 3-Oxopropyl]Amide (SAR107375)

Enzymatic activity of Crystal Structure Analysis of Thrombin in Complex with Compound D57, 5-Chlorothiophene-2-Carboxylic Acid [(S)-2-[2-Methyl-3-(2- Oxopyrrolidin-1-Yl)Benzenesulfonylamino]-3-(4-Methylpiperazin-1- Yl)- 3-Oxopropyl]Amide (SAR107375)

All present enzymatic activity of Crystal Structure Analysis of Thrombin in Complex with Compound D57, 5-Chlorothiophene-2-Carboxylic Acid [(S)-2-[2-Methyl-3-(2- Oxopyrrolidin-1-Yl)Benzenesulfonylamino]-3-(4-Methylpiperazin-1- Yl)- 3-Oxopropyl]Amide (SAR107375):
3.4.21.5;

Protein crystallography data

The structure of Crystal Structure Analysis of Thrombin in Complex with Compound D57, 5-Chlorothiophene-2-Carboxylic Acid [(S)-2-[2-Methyl-3-(2- Oxopyrrolidin-1-Yl)Benzenesulfonylamino]-3-(4-Methylpiperazin-1- Yl)- 3-Oxopropyl]Amide (SAR107375), PDB code: 4loy was solved by C.Stehlin-Gaon, Z.Bocskei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.58 / 1.77
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.522, 71.196, 73.140, 90.00, 100.91, 90.00
R / Rfree (%) 17.7 / 20.8

Other elements in 4loy:

The structure of Crystal Structure Analysis of Thrombin in Complex with Compound D57, 5-Chlorothiophene-2-Carboxylic Acid [(S)-2-[2-Methyl-3-(2- Oxopyrrolidin-1-Yl)Benzenesulfonylamino]-3-(4-Methylpiperazin-1- Yl)- 3-Oxopropyl]Amide (SAR107375) also contains other interesting chemical elements:

Fluorine (F) 1 atom
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure Analysis of Thrombin in Complex with Compound D57, 5-Chlorothiophene-2-Carboxylic Acid [(S)-2-[2-Methyl-3-(2- Oxopyrrolidin-1-Yl)Benzenesulfonylamino]-3-(4-Methylpiperazin-1- Yl)- 3-Oxopropyl]Amide (SAR107375) (pdb code 4loy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure Analysis of Thrombin in Complex with Compound D57, 5-Chlorothiophene-2-Carboxylic Acid [(S)-2-[2-Methyl-3-(2- Oxopyrrolidin-1-Yl)Benzenesulfonylamino]-3-(4-Methylpiperazin-1- Yl)- 3-Oxopropyl]Amide (SAR107375), PDB code: 4loy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4loy

Go back to Sodium Binding Sites List in 4loy
Sodium binding site 1 out of 2 in the Crystal Structure Analysis of Thrombin in Complex with Compound D57, 5-Chlorothiophene-2-Carboxylic Acid [(S)-2-[2-Methyl-3-(2- Oxopyrrolidin-1-Yl)Benzenesulfonylamino]-3-(4-Methylpiperazin-1- Yl)- 3-Oxopropyl]Amide (SAR107375)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Analysis of Thrombin in Complex with Compound D57, 5-Chlorothiophene-2-Carboxylic Acid [(S)-2-[2-Methyl-3-(2- Oxopyrrolidin-1-Yl)Benzenesulfonylamino]-3-(4-Methylpiperazin-1- Yl)- 3-Oxopropyl]Amide (SAR107375) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na302

b:24.6
occ:1.00
 O H:LYS224 2.3 21.5 1.0
O H:ARG221A 2.4 26.2 1.0
O H:HOH572 2.4 20.8 1.0
O H:HOH435 2.5 21.2 1.0
O H:HOH425 2.7 26.8 1.0
C H:LYS224 3.3 22.3 1.0
C H:ARG221A 3.4 28.1 1.0
N H:LYS224 3.8 20.9 1.0
N H:ARG221A 3.9 23.3 1.0
O H:HOH420 3.9 20.4 1.0
CA H:LYS224 4.0 19.4 1.0
O H:HOH411 4.0 23.0 1.0
O H:TYR184A 4.1 25.2 1.0
C H:ASP221 4.1 25.4 1.0
N H:ASP222 4.2 25.0 1.0
CA H:ARG221A 4.3 24.6 1.0
O H:HOH412 4.3 17.0 1.0
N H:TYR225 4.3 18.7 1.0
CA H:ASP222 4.4 25.3 1.0
N H:GLY223 4.4 24.9 1.0
CB H:LYS224 4.4 21.0 1.0
CA H:ASP221 4.4 21.4 1.0
O H:ASP221 4.6 25.3 1.0
C H:ASP222 4.6 27.9 1.0
CA H:TYR225 4.6 17.9 1.0
OD1 H:ASP221 4.7 21.5 1.0
C H:GLY223 4.8 26.4 1.0
CD2 H:TYR225 5.0 19.8 1.0

Sodium binding site 2 out of 2 in 4loy

Go back to Sodium Binding Sites List in 4loy
Sodium binding site 2 out of 2 in the Crystal Structure Analysis of Thrombin in Complex with Compound D57, 5-Chlorothiophene-2-Carboxylic Acid [(S)-2-[2-Methyl-3-(2- Oxopyrrolidin-1-Yl)Benzenesulfonylamino]-3-(4-Methylpiperazin-1- Yl)- 3-Oxopropyl]Amide (SAR107375)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure Analysis of Thrombin in Complex with Compound D57, 5-Chlorothiophene-2-Carboxylic Acid [(S)-2-[2-Methyl-3-(2- Oxopyrrolidin-1-Yl)Benzenesulfonylamino]-3-(4-Methylpiperazin-1- Yl)- 3-Oxopropyl]Amide (SAR107375) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na303

b:49.4
occ:1.00
 OG H:SER129B 2.6 42.9 1.0
O H:GLU127 2.7 23.2 1.0
C H:GLU127 3.4 25.2 1.0
CA H:GLU127 3.5 22.1 1.0
N H:SER129B 3.7 25.8 1.0
CB H:GLU127 3.8 24.2 1.0
CB H:ALA129A 3.8 26.3 1.0
CB H:SER129B 3.9 29.5 1.0
CA H:SER129B 4.2 25.8 1.0
C H:ALA129A 4.3 29.2 1.0
CG H:GLU127 4.4 32.1 1.0
CA H:ALA129A 4.6 24.5 1.0
N H:THR128 4.7 23.6 1.0
N H:GLU127 4.9 21.9 1.0
N H:ALA129A 4.9 23.1 1.0

Reference:

J.Meneyrol, M.Follmann, G.Lassalle, V.Wehner, G.Barre, T.Rousseaux, J.M.Altenburger, F.Petit, Z.Bocskei, H.Schreuder, N.Alet, J.P.Herault, L.Millet, F.Dol, P.Florian, P.Schaeffer, F.Sadoun, S.Klieber, C.Briot, F.Bono, J.M.Herbert. 5-Chlorothiophene-2-Carboxylic Acid [(S)-2-[2-Methyl-3-(2-Oxopyrrolidin-1-Yl) Benzenesulfonylamino]-3-(4-Methylpiperazin-1-Yl)-3- Oxopropyl]Amide (SAR107375), A Selective and Potent Orally Active Dual Thrombin and Factor Xa Inhibitor. J.Med.Chem. V. 56 9441 2013.
ISSN: ISSN 0022-2623
PubMed: 24175584
DOI: 10.1021/JM4005835
Page generated: Sun Aug 17 20:28:55 2025

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