Atomistry » Sodium » PDB 3h0n-3hwd » 3hpt
Atomistry »
  Sodium »
    PDB 3h0n-3hwd »
      3hpt »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy