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Sodium in PDB 3hpt: Crystal Structure of Human Fxa in Complex with (S)-2-Cyano-1-(2- Methylbenzofuran-5-Yl)-3-(2-Oxo-1-(2-Oxo-2-(Pyrrolidin-1-Yl)Ethyl) Azepan-3-Yl)Guanidine

Enzymatic activity of Crystal Structure of Human Fxa in Complex with (S)-2-Cyano-1-(2- Methylbenzofuran-5-Yl)-3-(2-Oxo-1-(2-Oxo-2-(Pyrrolidin-1-Yl)Ethyl) Azepan-3-Yl)Guanidine

All present enzymatic activity of Crystal Structure of Human Fxa in Complex with (S)-2-Cyano-1-(2- Methylbenzofuran-5-Yl)-3-(2-Oxo-1-(2-Oxo-2-(Pyrrolidin-1-Yl)Ethyl) Azepan-3-Yl)Guanidine:
3.4.21.6;

Protein crystallography data

The structure of Crystal Structure of Human Fxa in Complex with (S)-2-Cyano-1-(2- Methylbenzofuran-5-Yl)-3-(2-Oxo-1-(2-Oxo-2-(Pyrrolidin-1-Yl)Ethyl) Azepan-3-Yl)Guanidine, PDB code: 3hpt was solved by H.E.Klei, K.Ghosh, A.Rushith, K.Kish, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.980, 78.660, 73.670, 90.00, 102.49, 90.00
R / Rfree (%) 17.6 / 23.9

Other elements in 3hpt:

The structure of Crystal Structure of Human Fxa in Complex with (S)-2-Cyano-1-(2- Methylbenzofuran-5-Yl)-3-(2-Oxo-1-(2-Oxo-2-(Pyrrolidin-1-Yl)Ethyl) Azepan-3-Yl)Guanidine also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Fxa in Complex with (S)-2-Cyano-1-(2- Methylbenzofuran-5-Yl)-3-(2-Oxo-1-(2-Oxo-2-(Pyrrolidin-1-Yl)Ethyl) Azepan-3-Yl)Guanidine (pdb code 3hpt). 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 of Human Fxa in Complex with (S)-2-Cyano-1-(2- Methylbenzofuran-5-Yl)-3-(2-Oxo-1-(2-Oxo-2-(Pyrrolidin-1-Yl)Ethyl) Azepan-3-Yl)Guanidine, PDB code: 3hpt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3hpt

Go back to Sodium Binding Sites List in 3hpt
Sodium binding site 1 out of 2 in the Crystal Structure of Human Fxa in Complex with (S)-2-Cyano-1-(2- Methylbenzofuran-5-Yl)-3-(2-Oxo-1-(2-Oxo-2-(Pyrrolidin-1-Yl)Ethyl) Azepan-3-Yl)Guanidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Fxa in Complex with (S)-2-Cyano-1-(2- Methylbenzofuran-5-Yl)-3-(2-Oxo-1-(2-Oxo-2-(Pyrrolidin-1-Yl)Ethyl) Azepan-3-Yl)Guanidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3

b:35.4
occ:1.00
 O B:LYS224 2.2 30.8 1.0
O B:TYR185 2.3 33.7 1.0
O B:HOH317 2.4 36.9 1.0
O B:ARG222 2.4 35.8 1.0
O B:ASP185A 2.7 36.4 1.0
O B:HOH323 2.8 46.3 1.0
C B:LYS224 3.4 31.4 1.0
C B:ASP185A 3.4 36.2 1.0
C B:TYR185 3.4 33.5 1.0
C B:ARG222 3.6 36.0 1.0
N B:LYS224 3.7 32.5 1.0
CA B:ASP185A 3.9 35.9 1.0
CA B:LYS224 4.1 31.8 1.0
C B:ALA221 4.1 36.0 1.0
N B:ASP185A 4.1 34.8 1.0
O B:HOH361 4.2 32.5 1.0
N B:GLY223A 4.2 33.9 1.0
O B:ALA221 4.3 36.0 1.0
N B:ARG222 4.3 36.0 1.0
N B:THR185B 4.3 36.9 1.0
CA B:LYS223 4.4 35.4 1.0
N B:LYS223 4.4 35.8 1.0
N B:TYR225 4.5 30.7 1.0
CA B:ALA221 4.5 35.9 1.0
CA B:ARG222 4.5 35.9 0.5
CA B:ARG222 4.5 36.0 0.5
CA B:TYR185 4.6 32.6 1.0
C B:LYS223 4.6 34.5 1.0
CB B:LYS224 4.6 31.7 1.0
O B:LYS186 4.7 39.0 1.0
N B:TYR185 4.7 31.6 1.0
CA B:TYR225 4.7 30.1 1.0
C B:GLY223A 4.7 33.2 1.0
CA B:THR185B 4.8 37.5 1.0
CD1 B:TYR225 4.9 31.1 1.0
CB B:TYR185 5.0 32.1 1.0
CA B:GLY223A 5.0 33.5 1.0

Sodium binding site 2 out of 2 in 3hpt

Go back to Sodium Binding Sites List in 3hpt
Sodium binding site 2 out of 2 in the Crystal Structure of Human Fxa in Complex with (S)-2-Cyano-1-(2- Methylbenzofuran-5-Yl)-3-(2-Oxo-1-(2-Oxo-2-(Pyrrolidin-1-Yl)Ethyl) Azepan-3-Yl)Guanidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Fxa in Complex with (S)-2-Cyano-1-(2- Methylbenzofuran-5-Yl)-3-(2-Oxo-1-(2-Oxo-2-(Pyrrolidin-1-Yl)Ethyl) Azepan-3-Yl)Guanidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na4

b:49.2
occ:1.00
 O D:TYR185 2.3 35.9 1.0
O D:LYS224 2.4 31.7 1.0
O D:HOH342 2.5 41.2 1.0
O D:ARG222 2.5 37.7 1.0
O D:HOH330 2.7 40.7 1.0
O D:ASP185A 2.8 38.8 1.0
C D:TYR185 3.5 35.2 1.0
C D:ASP185A 3.5 38.5 1.0
C D:ARG222 3.6 37.7 1.0
C D:LYS224 3.6 32.0 1.0
N D:LYS224 3.9 33.5 1.0
O D:HOH384 4.0 36.6 1.0
C D:ALA221 4.0 37.6 1.0
CA D:ASP185A 4.1 38.0 1.0
N D:ARG222 4.1 37.5 1.0
O D:ALA221 4.2 37.9 1.0
N D:ASP185A 4.2 36.7 1.0
CA D:LYS224 4.3 32.4 1.0
N D:GLY223A 4.3 35.9 1.0
N D:LYS223 4.4 37.6 1.0
N D:THR185B 4.4 39.1 1.0
CA D:LYS223 4.4 37.5 1.0
CA D:ALA221 4.4 37.5 1.0
CA D:ARG222 4.5 37.7 1.0
O D:LYS186 4.6 39.0 1.0
C D:LYS223 4.6 36.7 1.0
CA D:TYR185 4.6 34.0 1.0
N D:TYR225 4.6 31.3 1.0
N D:TYR185 4.8 32.6 1.0
CA D:THR185B 4.8 39.3 1.0
CB D:LYS224 4.8 32.4 1.0
CA D:TYR225 4.8 30.4 1.0
C D:GLY223A 4.9 34.2 1.0

Reference:

Y.Shi, J.Zhang, M.Shi, S.P.O'connor, S.N.Bisaha, C.Li, D.Sitkoff, A.T.Pudzianowski, S.Chong, H.E.Klei, K.Kish, J.Yanchunas, E.C.Liu, K.S.Hartl, S.M.Seiler, T.E.Steinbacher, W.A.Schumacher, K.S.Atwal, P.D.Stein. Cyanoguanidine-Based Lactam Derivatives As A Novel Class of Orally Bioavailable Factor Xa Inhibitors. Bioorg.Med.Chem.Lett. V. 19 4034 2009.
ISSN: ISSN 0960-894X
PubMed: 19541481
DOI: 10.1016/J.BMCL.2009.06.014
Page generated: Mon Oct 7 10:25:42 2024

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