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Calcium 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
Sodium (Na) 2 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 2 in 3ens

Go back to Calcium Binding Sites List in 3ens
Calcium 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 Calcium with other atoms in the Ca 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:Ca302

b:44.2
occ:1.00
 O B:ASN72 2.8 39.4 1.0
OD1 B:ASP70 3.0 35.7 1.0
O B:GLN75 3.0 42.8 1.0
OE2 B:GLU80 3.1 39.0 1.0
CD B:GLU80 3.3 37.9 1.0
OD2 B:ASP70 3.3 35.0 1.0
CG B:ASP70 3.4 34.8 1.0
O B:THR73 3.6 41.5 1.0
OE1 B:GLU80 3.6 39.0 1.0
CA B:THR73 3.7 38.8 1.0
C B:GLN75 3.7 43.1 1.0
C B:THR73 3.8 40.5 1.0
C B:ASN72 3.8 38.5 1.0
CG B:GLU80 3.8 34.3 1.0
CA B:GLU76 4.1 43.6 1.0
N B:GLU76 4.1 43.4 1.0
N B:THR73 4.2 38.1 1.0
NH1 B:ARG67 4.5 31.4 1.0
N B:GLN75 4.6 42.4 1.0
N B:GLU77 4.6 42.2 1.0
CB B:ASP70 4.7 32.6 1.0
OE2 B:GLU76 4.7 49.0 1.0
N B:GLU74 4.7 40.7 1.0
CA B:GLN75 4.8 42.9 1.0
CB B:GLU80 4.9 32.8 1.0
C B:GLU76 4.9 42.6 1.0
CD B:ARG67 4.9 29.0 1.0
CB B:THR73 4.9 37.6 1.0
CZ B:ARG67 5.0 29.8 1.0

Calcium binding site 2 out of 2 in 3ens

Go back to Calcium Binding Sites List in 3ens
Calcium 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 Calcium with other atoms in the Ca 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:Ca302

b:45.6
occ:1.00
 O D:ASN72 2.7 40.1 1.0
O D:GLN75 2.8 42.1 1.0
OE2 D:GLU80 2.9 39.5 1.0
OD1 D:ASP70 3.0 36.0 1.0
OD2 D:ASP70 3.1 35.6 1.0
CG D:ASP70 3.2 35.2 1.0
CD D:GLU80 3.2 38.3 1.0
OE1 D:GLU80 3.8 38.4 1.0
C D:ASN72 3.8 39.4 1.0
CG D:GLU80 3.8 35.4 1.0
C D:GLN75 3.9 43.1 1.0
CA D:GLU76 4.1 42.2 1.0
N D:GLU77 4.1 41.5 1.0
CA D:THR73 4.3 39.6 1.0
CB D:ASP70 4.4 32.7 1.0
N D:GLU76 4.4 43.5 1.0
N D:THR73 4.5 39.2 1.0
O D:THR73 4.5 42.2 1.0
C D:THR73 4.6 41.3 1.0
C D:GLU76 4.6 41.8 1.0
CG D:GLU77 4.7 42.2 1.0
N D:ASN72 4.8 36.8 1.0
OE1 D:GLU76 4.8 41.9 1.0
CB D:GLU80 4.8 33.0 1.0
CA D:ASP70 4.8 32.6 1.0
CA D:ASN72 4.9 38.6 1.0
CB D:GLU77 5.0 41.5 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: Tue Jul 8 11:57:59 2025

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