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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

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