Atomistry » Calcium » PDB 3hjb-3hz3 » 3hpt
Atomistry »
  Calcium »
    PDB 3hjb-3hz3 »
      3hpt »

Calcium 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:

Sodium (Na) 2 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 2 in 3hpt

Go back to Calcium Binding Sites List in 3hpt
Calcium 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 Calcium with other atoms in the Ca 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:Ca249

b:86.3
occ:1.00
 OE2 B:GLU80 2.2 47.2 1.0
O B:ASN72 2.2 50.5 1.0
O B:GLN75 2.4 56.6 1.0
OD1 B:ASP70 2.6 39.9 1.0
C B:ASN72 3.3 50.4 1.0
CD B:GLU80 3.4 46.5 1.0
CG B:ASP70 3.5 40.5 1.0
C B:GLN75 3.6 56.4 1.0
OD2 B:ASP70 3.8 42.6 1.0
CA B:THR73 3.8 52.4 1.0
CG B:GLU80 4.0 43.9 1.0
N B:THR73 4.0 51.2 1.0
C B:THR73 4.2 53.3 1.0
CA B:GLU76 4.2 56.2 1.0
N B:GLU77 4.3 55.6 1.0
O B:THR73 4.3 53.6 1.0
N B:GLU76 4.3 56.4 1.0
OE1 B:GLU80 4.4 47.8 1.0
OE1 B:GLU77 4.4 59.3 1.0
CA B:ASN72 4.5 49.7 1.0
N B:ASN72 4.5 48.2 1.0
N B:GLN75 4.6 56.1 1.0
CG B:GLU77 4.6 56.0 1.0
CB B:ASP70 4.6 39.7 1.0
CA B:GLN75 4.7 56.4 1.0
C B:GLU76 4.8 55.9 1.0
N B:GLU74 4.9 54.3 1.0
CD B:GLU77 4.9 58.4 1.0
CA B:ASP70 4.9 39.8 1.0
N B:ARG71 5.0 43.3 1.0

Calcium binding site 2 out of 2 in 3hpt

Go back to Calcium Binding Sites List in 3hpt
Calcium 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 Calcium with other atoms in the Ca 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:Ca249

b:71.4
occ:1.00
 O D:ASN72 2.3 49.2 1.0
OE2 D:GLU80 2.4 46.3 1.0
OD1 D:ASP70 2.6 38.8 1.0
O D:HOH491 2.7 48.6 1.0
O D:GLN75 2.9 58.6 1.0
O D:HOH360 3.0 54.7 1.0
C D:ASN72 3.3 48.9 1.0
CD D:GLU80 3.4 45.0 1.0
CG D:ASP70 3.5 38.4 1.0
CG D:GLU80 3.8 42.4 1.0
N D:GLU77 3.8 56.5 1.0
C D:GLN75 3.9 58.4 1.0
OD2 D:ASP70 3.9 39.9 1.0
CA D:GLU76 3.9 57.9 1.0
N D:THR73 4.1 50.8 1.0
CA D:THR73 4.1 52.8 1.0
N D:ASN72 4.1 44.9 1.0
CA D:ASN72 4.2 47.6 1.0
N D:GLU76 4.3 58.2 1.0
C D:GLU76 4.4 57.4 1.0
C D:THR73 4.4 54.2 1.0
OE1 D:GLU80 4.5 46.5 1.0
O D:THR73 4.6 54.6 1.0
CB D:ASP70 4.6 37.2 1.0
CB D:GLU77 4.7 55.5 1.0
CB D:ASN72 4.7 47.7 1.0
N D:ARG71 4.7 40.5 1.0
O D:HOH448 4.8 40.7 1.0
CA D:ASP70 4.8 37.3 1.0
CA D:GLU77 4.9 55.5 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: Sat Jul 13 11:09:30 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