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Chlorine 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:

Calcium (Ca) 2 atoms
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 3ens

Go back to Chlorine Binding Sites List in 3ens
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl301

b:27.9
occ:1.00
 CL36 B:ENS301 0.0 27.9 1.0
C5 B:ENS301 1.8 26.7 1.0
C7 B:ENS301 2.8 26.7 1.0
C6 B:ENS301 2.8 27.1 1.0
CA B:GLY226 3.2 24.2 1.0
C3 B:ENS301 3.3 25.9 1.0
CB B:ALA190 3.6 26.0 1.0
O B:TRP215 3.6 24.5 1.0
N B:ILE227 3.7 22.9 1.0
C B:GLY226 3.8 23.1 1.0
C8 B:ENS301 3.9 27.2 1.0
N27 B:ENS301 3.9 27.7 1.0
CG1 B:VAL213 3.9 23.3 1.0
O B:ILE227 4.2 22.0 1.0
OD2 B:ASP189 4.2 26.4 1.0
CZ B:TYR228 4.2 22.5 1.0
CE1 B:TYR228 4.3 22.4 1.0
OH B:TYR228 4.3 22.9 1.0
C B:TRP215 4.4 25.1 1.0
CA B:ALA190 4.5 26.8 1.0
N B:GLY226 4.5 24.3 1.0
C B:ALA190 4.7 27.3 1.0
O B:ALA190 4.7 27.9 1.0
N B:ALA190 4.7 27.0 1.0
C B:ILE227 4.7 21.9 1.0
O B:GLY226 4.7 22.7 1.0
C2 B:ENS301 4.7 26.1 1.0
O B:HOH397 4.7 24.3 1.0
CA B:ILE227 4.8 22.5 1.0
N B:TRP215 4.8 23.1 1.0
CE2 B:TYR228 4.8 22.1 1.0
CD1 B:TYR228 4.9 21.9 1.0
N B:SER214 5.0 21.9 1.0

Chlorine binding site 2 out of 2 in 3ens

Go back to Chlorine Binding Sites List in 3ens
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl301

b:28.7
occ:1.00
 CL36 D:ENS301 0.0 28.7 1.0
C5 D:ENS301 1.8 28.4 1.0
C7 D:ENS301 2.8 28.4 1.0
C6 D:ENS301 2.8 28.7 1.0
CA D:GLY226 3.1 25.5 1.0
C3 D:ENS301 3.3 27.3 1.0
N D:ILE227 3.6 24.5 1.0
CB D:ALA190 3.7 28.2 1.0
C D:GLY226 3.7 24.5 1.0
O D:TRP215 3.7 24.9 1.0
C8 D:ENS301 3.9 28.9 1.0
N27 D:ENS301 4.0 29.0 1.0
CG1 D:VAL213 4.0 24.0 1.0
O D:ILE227 4.1 22.8 1.0
OD2 D:ASP189 4.1 29.2 1.0
CE1 D:TYR228 4.2 23.3 1.0
CZ D:TYR228 4.2 23.1 1.0
OH D:TYR228 4.3 23.3 1.0
C D:TRP215 4.4 25.6 1.0
N D:GLY226 4.4 26.9 1.0
CA D:ALA190 4.6 29.1 1.0
C D:ILE227 4.7 22.8 1.0
O D:GLY226 4.7 23.9 1.0
C2 D:ENS301 4.7 27.5 1.0
CA D:ILE227 4.8 23.2 1.0
N D:ALA190 4.8 29.3 1.0
C D:ALA190 4.8 29.4 1.0
CD1 D:TYR228 4.8 22.7 1.0
CE2 D:TYR228 4.8 22.6 1.0
CG D:ASP189 4.9 29.8 1.0
N D:TRP215 4.9 23.5 1.0
O D:HOH334 4.9 28.7 1.0
OD1 D:ASP189 5.0 29.7 1.0
O D:ALA190 5.0 30.1 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: Fri Jul 11 04:49:50 2025

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