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Calcium in PDB 3k9x: X-Ray Crystal Structure of Human Fxa in Complex with (S)-N-((2- Methylbenzofuran-5-Ylamino)(2-Oxo-1-(2-Oxo-2- (Pyrrolidin-1-Yl) Ethyl)Azepan-3- Ylamino)Methylene)Nicotinamide

Enzymatic activity of X-Ray Crystal Structure of Human Fxa in Complex with (S)-N-((2- Methylbenzofuran-5-Ylamino)(2-Oxo-1-(2-Oxo-2- (Pyrrolidin-1-Yl) Ethyl)Azepan-3- Ylamino)Methylene)Nicotinamide

All present enzymatic activity of X-Ray Crystal Structure of Human Fxa in Complex with (S)-N-((2- Methylbenzofuran-5-Ylamino)(2-Oxo-1-(2-Oxo-2- (Pyrrolidin-1-Yl) Ethyl)Azepan-3- Ylamino)Methylene)Nicotinamide:
3.4.21.6;

Protein crystallography data

The structure of X-Ray Crystal Structure of Human Fxa in Complex with (S)-N-((2- Methylbenzofuran-5-Ylamino)(2-Oxo-1-(2-Oxo-2- (Pyrrolidin-1-Yl) Ethyl)Azepan-3- Ylamino)Methylene)Nicotinamide, PDB code: 3k9x was solved by H.E.Klei, K.Kish, K.Ghosh, A.Rushith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.54 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.263, 77.630, 73.732, 90.00, 102.63, 90.00
R / Rfree (%) 17.6 / 24

Other elements in 3k9x:

The structure of X-Ray Crystal Structure of Human Fxa in Complex with (S)-N-((2- Methylbenzofuran-5-Ylamino)(2-Oxo-1-(2-Oxo-2- (Pyrrolidin-1-Yl) Ethyl)Azepan-3- Ylamino)Methylene)Nicotinamide also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Crystal Structure of Human Fxa in Complex with (S)-N-((2- Methylbenzofuran-5-Ylamino)(2-Oxo-1-(2-Oxo-2- (Pyrrolidin-1-Yl) Ethyl)Azepan-3- Ylamino)Methylene)Nicotinamide (pdb code 3k9x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the X-Ray Crystal Structure of Human Fxa in Complex with (S)-N-((2- Methylbenzofuran-5-Ylamino)(2-Oxo-1-(2-Oxo-2- (Pyrrolidin-1-Yl) Ethyl)Azepan-3- Ylamino)Methylene)Nicotinamide, PDB code: 3k9x:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3k9x

Go back to Calcium Binding Sites List in 3k9x
Calcium binding site 1 out of 2 in the X-Ray Crystal Structure of Human Fxa in Complex with (S)-N-((2- Methylbenzofuran-5-Ylamino)(2-Oxo-1-(2-Oxo-2- (Pyrrolidin-1-Yl) Ethyl)Azepan-3- Ylamino)Methylene)Nicotinamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Crystal Structure of Human Fxa in Complex with (S)-N-((2- Methylbenzofuran-5-Ylamino)(2-Oxo-1-(2-Oxo-2- (Pyrrolidin-1-Yl) Ethyl)Azepan-3- Ylamino)Methylene)Nicotinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca249

b:49.1
occ:1.00
 OD1 B:ASP70 2.3 36.0 1.0
O B:ASN72 2.4 37.8 1.0
OE1 B:GLU80 2.5 49.1 1.0
O B:GLN75 2.5 53.9 1.0
O B:HOH567 2.6 43.2 1.0
OE2 B:GLU80 2.7 55.3 1.0
CD B:GLU80 2.8 51.6 1.0
O B:HOH439 3.1 42.2 1.0
CG B:ASP70 3.2 34.8 1.0
C B:GLN75 3.4 55.9 1.0
C B:ASN72 3.4 37.1 1.0
OD2 B:ASP70 3.5 35.0 1.0
N B:GLU76 3.9 53.4 1.0
CA B:GLU76 3.9 57.8 1.0
CG B:GLU80 4.2 44.6 1.0
CA B:THR73 4.2 37.0 1.0
N B:ASN72 4.3 33.2 1.0
N B:THR73 4.3 34.4 1.0
N B:GLU77 4.3 56.3 1.0
C B:GLU76 4.3 57.1 1.0
CA B:ASN72 4.3 35.2 1.0
CB B:ASP70 4.4 30.8 1.0
N B:GLN75 4.4 53.2 1.0
CA B:GLN75 4.4 52.5 1.0
C B:THR73 4.6 44.5 1.0
CA B:ASP70 4.6 28.0 1.0
CB B:ASN72 4.7 37.6 1.0
CB B:GLU77 4.8 57.9 1.0
N B:ARG71 4.9 31.1 1.0
CB B:GLN75 4.9 53.5 1.0
OE2 B:GLU76 4.9 60.8 1.0
CB B:GLU80 4.9 37.4 1.0
N B:GLU74 5.0 45.5 1.0

Calcium binding site 2 out of 2 in 3k9x

Go back to Calcium Binding Sites List in 3k9x
Calcium binding site 2 out of 2 in the X-Ray Crystal Structure of Human Fxa in Complex with (S)-N-((2- Methylbenzofuran-5-Ylamino)(2-Oxo-1-(2-Oxo-2- (Pyrrolidin-1-Yl) Ethyl)Azepan-3- Ylamino)Methylene)Nicotinamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Crystal Structure of Human Fxa in Complex with (S)-N-((2- Methylbenzofuran-5-Ylamino)(2-Oxo-1-(2-Oxo-2- (Pyrrolidin-1-Yl) Ethyl)Azepan-3- Ylamino)Methylene)Nicotinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca249

b:61.2
occ:1.00
 OD1 D:ASP70 2.4 43.3 1.0
O D:ASN72 2.4 42.9 1.0
OE1 D:GLU80 2.4 54.0 1.0
O D:HOH662 2.5 47.4 1.0
O D:HOH882 2.6 48.2 1.0
CD D:GLU80 2.9 55.3 1.0
OE2 D:GLU80 3.0 55.7 1.0
O D:GLN75 3.0 63.0 1.0
CG D:ASP70 3.2 41.4 1.0
OD2 D:ASP70 3.5 42.1 1.0
C D:GLN75 3.5 63.4 1.0
C D:ASN72 3.5 39.8 1.0
N D:GLU76 4.0 66.7 1.0
CA D:THR73 4.0 42.1 1.0
N D:GLN75 4.1 53.2 1.0
CG D:GLU80 4.2 47.8 1.0
CA D:GLU76 4.2 64.2 1.0
N D:THR73 4.2 35.6 1.0
C D:THR73 4.3 49.1 1.0
N D:GLU77 4.3 62.0 1.0
CA D:GLN75 4.4 57.4 1.0
CB D:ASP70 4.5 35.2 1.0
N D:ASN72 4.5 36.9 1.0
CA D:ASN72 4.6 40.4 1.0
N D:GLU74 4.7 45.9 1.0
O D:THR73 4.7 49.4 1.0
C D:GLU76 4.8 64.8 1.0
CA D:ASP70 4.9 33.7 1.0
CB D:GLU80 4.9 40.4 1.0
OE2 D:GLU76 5.0 69.8 1.0

Reference:

Y.Shi, C.Li, S.P.O'connor, J.Zhang, M.Shi, S.N.Bisaha, Y.Wang, D.Sitkoff, A.T.Pudzianowski, C.Huang, 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. Aroylguanidine-Based Factor Xa Inhibitors: the Discovery of Bms-344577 Bioorg.Med.Chem.Lett. V. 19 6882 2009.
ISSN: ISSN 0960-894X
PubMed: 19896847
DOI: 10.1016/J.BMCL.2009.10.084
Page generated: Tue Jul 8 13:46:18 2025

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