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Sodium in PDB 3ens: Crystal Structure of Human Fxa in Complex with Methyl (2Z)-3-[(3- Chloro-1H-Indol-7-Yl)Amino]-2-Cyano-3-{[(3S)-2-Oxo-1-(2-Oxo-2- Pyrrolidin-1-Ylethyl)Azepan-3-Yl]Amino}Acrylate

Enzymatic activity of Crystal Structure of Human Fxa in Complex with Methyl (2Z)-3-[(3- Chloro-1H-Indol-7-Yl)Amino]-2-Cyano-3-{[(3S)-2-Oxo-1-(2-Oxo-2- Pyrrolidin-1-Ylethyl)Azepan-3-Yl]Amino}Acrylate

All present enzymatic activity of Crystal Structure of Human Fxa in Complex with Methyl (2Z)-3-[(3- Chloro-1H-Indol-7-Yl)Amino]-2-Cyano-3-{[(3S)-2-Oxo-1-(2-Oxo-2- Pyrrolidin-1-Ylethyl)Azepan-3-Yl]Amino}Acrylate:
3.4.21.6;

Protein crystallography data

The structure of Crystal Structure of Human Fxa in Complex with Methyl (2Z)-3-[(3- Chloro-1H-Indol-7-Yl)Amino]-2-Cyano-3-{[(3S)-2-Oxo-1-(2-Oxo-2- Pyrrolidin-1-Ylethyl)Azepan-3-Yl]Amino}Acrylate, PDB code: 3ens was solved by H.E.Klei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.03 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.311, 78.861, 73.850, 90.00, 102.82, 90.00
R / Rfree (%) 22.3 / 28.6

Other elements in 3ens:

The structure of Crystal Structure of Human Fxa in Complex with Methyl (2Z)-3-[(3- Chloro-1H-Indol-7-Yl)Amino]-2-Cyano-3-{[(3S)-2-Oxo-1-(2-Oxo-2- Pyrrolidin-1-Ylethyl)Azepan-3-Yl]Amino}Acrylate also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Fxa in Complex with Methyl (2Z)-3-[(3- Chloro-1H-Indol-7-Yl)Amino]-2-Cyano-3-{[(3S)-2-Oxo-1-(2-Oxo-2- Pyrrolidin-1-Ylethyl)Azepan-3-Yl]Amino}Acrylate (pdb code 3ens). 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 Methyl (2Z)-3-[(3- Chloro-1H-Indol-7-Yl)Amino]-2-Cyano-3-{[(3S)-2-Oxo-1-(2-Oxo-2- Pyrrolidin-1-Ylethyl)Azepan-3-Yl]Amino}Acrylate, PDB code: 3ens:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3ens

Go back to Sodium Binding Sites List in 3ens
Sodium binding site 1 out of 2 in the Crystal Structure of Human Fxa in Complex with Methyl (2Z)-3-[(3- Chloro-1H-Indol-7-Yl)Amino]-2-Cyano-3-{[(3S)-2-Oxo-1-(2-Oxo-2- Pyrrolidin-1-Ylethyl)Azepan-3-Yl]Amino}Acrylate


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 Methyl (2Z)-3-[(3- Chloro-1H-Indol-7-Yl)Amino]-2-Cyano-3-{[(3S)-2-Oxo-1-(2-Oxo-2- Pyrrolidin-1-Ylethyl)Azepan-3-Yl]Amino}Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:29.7
occ:1.00
 O B:TYR185 3.0 26.6 1.0
O B:ARG222 3.0 28.1 1.0
O B:ASP185A 3.1 28.4 1.0
O B:LYS186 3.4 28.3 1.0
C B:ASP185A 3.5 27.9 1.0
C B:ALA221 3.5 28.9 1.0
O B:LYS224 3.6 26.2 1.0
O B:ALA221 3.6 29.2 1.0
C B:ARG222 3.6 28.4 1.0
C B:TYR185 3.7 26.8 1.0
CA B:ALA221 3.8 28.6 1.0
N B:THR185B 3.9 27.9 1.0
N B:ARG222 3.9 28.6 1.0
CA B:THR185B 4.1 28.2 1.0
C B:THR185B 4.1 27.9 1.0
O B:HOH312 4.2 25.7 1.0
N B:LYS223 4.2 28.3 1.0
CA B:ASP185A 4.2 27.3 1.0
N B:ASP185A 4.3 27.1 1.0
O B:THR185B 4.3 28.5 1.0
CA B:ARG222 4.4 28.4 1.0
CA B:LYS223 4.4 28.5 1.0
N B:LYS186 4.5 27.8 1.0
CB B:ALA221 4.5 28.8 1.0
C B:LYS186 4.5 28.1 1.0
CB B:TYR185 4.6 26.6 1.0
CA B:TYR185 4.6 26.0 1.0
C B:LYS224 4.7 26.2 1.0
OE1 B:GLN187 4.8 29.7 1.0
N B:LYS224 4.9 27.0 1.0
N B:GLY223A 4.9 27.4 1.0
N B:TYR185 4.9 25.8 1.0
N B:ALA221 5.0 28.3 1.0
O B:GLU188 5.0 26.8 1.0

Sodium binding site 2 out of 2 in 3ens

Go back to Sodium Binding Sites List in 3ens
Sodium binding site 2 out of 2 in the Crystal Structure of Human Fxa in Complex with Methyl (2Z)-3-[(3- Chloro-1H-Indol-7-Yl)Amino]-2-Cyano-3-{[(3S)-2-Oxo-1-(2-Oxo-2- Pyrrolidin-1-Ylethyl)Azepan-3-Yl]Amino}Acrylate


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 Methyl (2Z)-3-[(3- Chloro-1H-Indol-7-Yl)Amino]-2-Cyano-3-{[(3S)-2-Oxo-1-(2-Oxo-2- Pyrrolidin-1-Ylethyl)Azepan-3-Yl]Amino}Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na303

b:31.8
occ:1.00
 O D:TYR185 3.0 29.1 1.0
O D:ASP185A 3.1 31.2 1.0
O D:ARG222 3.1 31.2 1.0
O D:LYS186 3.2 31.0 1.0
O D:ALA221 3.3 31.9 1.0
C D:ALA221 3.4 31.7 1.0
C D:ASP185A 3.5 30.7 1.0
C D:ARG222 3.7 31.4 1.0
CA D:ALA221 3.7 31.5 1.0
C D:TYR185 3.8 29.4 1.0
N D:THR185B 3.8 31.2 1.0
O D:LYS224 3.9 28.8 1.0
N D:ARG222 3.9 31.4 1.0
C D:THR185B 4.0 31.5 1.0
CA D:THR185B 4.1 31.6 1.0
C D:LYS186 4.2 30.9 1.0
O D:THR185B 4.3 32.2 1.0
CA D:ASP185A 4.3 30.3 1.0
N D:LYS186 4.3 30.9 1.0
N D:LYS223 4.4 31.5 1.0
N D:ASP185A 4.4 30.1 1.0
CA D:ARG222 4.4 31.1 1.0
CB D:ALA221 4.5 31.9 1.0
CB D:TYR185 4.5 29.4 1.0
CA D:LYS223 4.6 31.4 1.0
OE1 D:GLN187 4.6 33.3 1.0
CA D:TYR185 4.6 28.9 1.0
O D:GLU188 4.8 30.1 1.0
N D:ALA221 4.9 31.2 1.0
CA D:LYS186 4.9 31.0 1.0
N D:TYR185 5.0 28.0 1.0

Reference:

Y.Shi, D.Sitkoff, J.Zhang, H.E.Klei, K.Kish, E.C.Liu, K.S.Hartl, S.M.Seiler, M.Chang, C.Huang, S.Youssef, T.E.Steinbacher, W.A.Schumacher, N.Grazier, A.Pudzianowski, A.Apedo, L.Discenza, J.Yanchunas, P.D.Stein, K.S.Atwal. Design, Structure-Activity Relationships, X-Ray Crystal Structure, and Energetic Contributions of A Critical P1 Pharmacophore: 3-Chloroindole-7-Yl-Based Factor Xa Inhibitors. J.Med.Chem. V. 51 7541 2008.
ISSN: ISSN 0022-2623
PubMed: 18998662
DOI: 10.1021/JM800855X
Page generated: Mon Oct 7 08:52:16 2024

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