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Fluorine 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:

Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total only one binding site of Fluorine was 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:

Fluorine binding site 1 out of 1 in 4loy

Go back to Fluorine Binding Sites List in 4loy
Fluorine binding site 1 out of 1 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 Fluorine with other atoms in the F 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:F304

b:37.4
occ:1.00
 F13 H:6XS304 0.0 37.4 1.0
C11 H:6XS304 1.3 34.4 1.0
C12 H:6XS304 2.4 32.5 1.0
C10 H:6XS304 2.4 31.5 1.0
NE1 H:TRP60D 3.4 38.4 1.0
CZ2 H:TRP60D 3.4 39.4 1.0
CE2 H:TRP60D 3.6 39.8 1.0
C7 H:6XS304 3.6 29.4 1.0
C21 H:6XS304 3.7 32.7 1.0
C9 H:6XS304 3.7 27.8 1.0
OH H:TYR60A 3.7 30.7 1.0
O H:HOH610 3.8 40.2 1.0
CE2 H:TYR60A 3.8 25.9 1.0
C25 H:6XS304 4.0 36.3 1.0
CZ H:TYR60A 4.1 32.0 1.0
C8 H:6XS304 4.1 28.8 1.0
N22 H:6XS304 4.3 34.0 1.0
CH2 H:TRP60D 4.4 39.8 1.0
CD1 H:TRP60D 4.5 38.9 1.0
C23 H:6XS304 4.5 30.2 1.0
O H:HOH591 4.6 49.7 1.0
CD2 H:TRP60D 4.7 35.7 1.0
N3 H:6XS304 4.8 30.2 1.0
C20 H:6XS304 4.8 30.2 1.0
CD2 H:TYR60A 4.9 24.5 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: Thu Aug 1 03:29:19 2024

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