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Sodium in PDB 3k9x: X-Ray Crystal Structure of Human Fxa in Complex with (S)-N-((2- Methylbenzofuran-5-Ylamino)(2-Oxo-1-(2-Oxo-2- (Pyrrolidin-1-Yl) Ethyl)Azepan-3- Ylamino)Methylene)Nicotinamide

Enzymatic activity of X-Ray Crystal Structure of Human Fxa in Complex with (S)-N-((2- Methylbenzofuran-5-Ylamino)(2-Oxo-1-(2-Oxo-2- (Pyrrolidin-1-Yl) Ethyl)Azepan-3- Ylamino)Methylene)Nicotinamide

All present enzymatic activity of X-Ray Crystal Structure of Human Fxa in Complex with (S)-N-((2- Methylbenzofuran-5-Ylamino)(2-Oxo-1-(2-Oxo-2- (Pyrrolidin-1-Yl) Ethyl)Azepan-3- Ylamino)Methylene)Nicotinamide:
3.4.21.6;

Protein crystallography data

The structure of X-Ray Crystal Structure of Human Fxa in Complex with (S)-N-((2- Methylbenzofuran-5-Ylamino)(2-Oxo-1-(2-Oxo-2- (Pyrrolidin-1-Yl) Ethyl)Azepan-3- Ylamino)Methylene)Nicotinamide, PDB code: 3k9x was solved by H.E.Klei, K.Kish, K.Ghosh, A.Rushith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.54 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.263, 77.630, 73.732, 90.00, 102.63, 90.00
R / Rfree (%) 17.6 / 24

Other elements in 3k9x:

The structure of X-Ray Crystal Structure of Human Fxa in Complex with (S)-N-((2- Methylbenzofuran-5-Ylamino)(2-Oxo-1-(2-Oxo-2- (Pyrrolidin-1-Yl) Ethyl)Azepan-3- Ylamino)Methylene)Nicotinamide also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Crystal Structure of Human Fxa in Complex with (S)-N-((2- Methylbenzofuran-5-Ylamino)(2-Oxo-1-(2-Oxo-2- (Pyrrolidin-1-Yl) Ethyl)Azepan-3- Ylamino)Methylene)Nicotinamide (pdb code 3k9x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Crystal Structure of Human Fxa in Complex with (S)-N-((2- Methylbenzofuran-5-Ylamino)(2-Oxo-1-(2-Oxo-2- (Pyrrolidin-1-Yl) Ethyl)Azepan-3- Ylamino)Methylene)Nicotinamide, PDB code: 3k9x:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3k9x

Go back to Sodium Binding Sites List in 3k9x
Sodium binding site 1 out of 2 in the X-Ray Crystal Structure of Human Fxa in Complex with (S)-N-((2- Methylbenzofuran-5-Ylamino)(2-Oxo-1-(2-Oxo-2- (Pyrrolidin-1-Yl) Ethyl)Azepan-3- Ylamino)Methylene)Nicotinamide


Mono view


Stereo pair view

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

b:25.4
occ:1.00
 O B:TYR185 2.3 22.2 1.0
O B:LYS224 2.4 20.8 1.0
O B:ARG222 2.5 23.3 1.0
O B:HOH504 2.6 25.6 1.0
O B:ASP185A 2.6 23.5 1.0
O B:HOH304 2.8 23.9 1.0
C B:ASP185A 3.4 28.9 1.0
C B:TYR185 3.5 25.4 1.0
C B:ARG222 3.5 25.8 1.0
C B:LYS224 3.6 20.2 1.0
N B:LYS224 3.8 22.8 1.0
CA B:ASP185A 4.0 29.7 1.0
C B:ALA221 4.0 25.2 1.0
N B:ARG222 4.0 21.2 1.0
N B:GLY223A 4.1 24.2 1.0
O B:HOH283 4.1 25.1 1.0
N B:ASP185A 4.2 23.9 1.0
N B:THR185B 4.2 26.2 1.0
CA B:LYS223 4.2 25.4 1.0
CA B:LYS224 4.2 18.4 1.0
O B:ALA221 4.3 24.9 1.0
N B:LYS223 4.3 24.8 1.0
CA B:ALA221 4.4 23.1 1.0
C B:LYS223 4.4 24.8 1.0
CA B:ARG222 4.5 25.3 1.0
CA B:TYR185 4.6 22.5 1.0
CA B:THR185B 4.6 29.2 1.0
N B:TYR225 4.7 18.9 1.0
O B:LYS186 4.7 25.1 1.0
N B:TYR185 4.7 20.5 1.0
C B:GLY223A 4.7 26.3 1.0
CB B:LYS224 4.8 19.8 1.0
CA B:TYR225 4.9 19.8 1.0
CA B:GLY223A 4.9 25.9 1.0
CB B:TYR185 5.0 23.1 1.0

Sodium binding site 2 out of 2 in 3k9x

Go back to Sodium Binding Sites List in 3k9x
Sodium binding site 2 out of 2 in the X-Ray Crystal Structure of Human Fxa in Complex with (S)-N-((2- Methylbenzofuran-5-Ylamino)(2-Oxo-1-(2-Oxo-2- (Pyrrolidin-1-Yl) Ethyl)Azepan-3- Ylamino)Methylene)Nicotinamide


Mono view


Stereo pair view

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

b:29.9
occ:1.00
 O D:LYS224 2.4 23.2 1.0
O D:TYR185 2.4 27.5 1.0
O D:HOH399 2.5 25.0 1.0
O D:ARG222 2.5 26.1 1.0
O D:ASP185A 2.8 30.7 1.0
O D:HOH271 2.8 28.7 1.0
C D:ASP185A 3.4 29.9 1.0
C D:ARG222 3.5 29.5 1.0
C D:LYS224 3.5 26.2 1.0
C D:TYR185 3.5 29.1 1.0
N D:LYS224 3.8 25.4 1.0
CA D:ASP185A 3.9 30.7 1.0
O D:HOH296 4.0 25.6 1.0
C D:ALA221 4.1 29.1 1.0
N D:ARG222 4.1 26.2 1.0
CA D:LYS224 4.2 21.0 1.0
N D:ASP185A 4.2 28.2 1.0
CA D:LYS223 4.2 28.2 1.0
N D:GLY223A 4.2 26.1 1.0
N D:LYS223 4.3 28.8 1.0
O D:ALA221 4.3 31.0 1.0
N D:THR185B 4.3 32.1 1.0
CA D:ARG222 4.4 28.3 1.0
C D:LYS223 4.4 25.8 1.0
CA D:ALA221 4.5 30.1 1.0
O D:LYS186 4.6 29.3 1.0
N D:TYR225 4.6 21.4 1.0
CA D:TYR185 4.6 26.4 1.0
CB D:LYS224 4.7 21.1 1.0
CA D:THR185B 4.7 30.9 1.0
N D:TYR185 4.7 27.2 1.0
C D:GLY223A 4.8 26.4 1.0
CA D:TYR225 4.8 19.6 1.0
CB D:TYR185 4.9 27.6 1.0
CD1 D:TYR225 4.9 26.1 1.0
CA D:GLY223A 5.0 30.7 1.0

Reference:

Y.Shi, C.Li, S.P.O'connor, J.Zhang, M.Shi, S.N.Bisaha, Y.Wang, D.Sitkoff, A.T.Pudzianowski, C.Huang, 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. Aroylguanidine-Based Factor Xa Inhibitors: the Discovery of Bms-344577 Bioorg.Med.Chem.Lett. V. 19 6882 2009.
ISSN: ISSN 0960-894X
PubMed: 19896847
DOI: 10.1016/J.BMCL.2009.10.084
Page generated: Mon Oct 7 11:12:37 2024

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