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Calcium in PDB 2y80: Structure and Property Based Design of Factor Xa Inhibitors: Pyrrolidin-2-Ones with Aminoindane and Phenylpyrrolidine P4 Motifs

Enzymatic activity of Structure and Property Based Design of Factor Xa Inhibitors: Pyrrolidin-2-Ones with Aminoindane and Phenylpyrrolidine P4 Motifs

All present enzymatic activity of Structure and Property Based Design of Factor Xa Inhibitors: Pyrrolidin-2-Ones with Aminoindane and Phenylpyrrolidine P4 Motifs:
3.4.21.6;

Protein crystallography data

The structure of Structure and Property Based Design of Factor Xa Inhibitors: Pyrrolidin-2-Ones with Aminoindane and Phenylpyrrolidine P4 Motifs, PDB code: 2y80 was solved by R.J.Young, C.Adams, M.Blows, D.Brown, C.L.Burns-Kurtis, L.Chaudry, C.Chan, M.A.Convery, D.E.Davies, A.M.Exall, G.Foster, J.D.Harling, E.Hortense, W.R.Irving, S.Irvine, S.Jackson, S.Kleanthous, A.J.Pateman, A.N.Patikis, T.J.Roethka, S.Senger, G.J.Stelman, J.R.Toomey, R.I.West, C.Whittaker, P.Zhou, N.S.Watson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.727, 72.012, 78.689, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 24.1

Other elements in 2y80:

The structure of Structure and Property Based Design of Factor Xa Inhibitors: Pyrrolidin-2-Ones with Aminoindane and Phenylpyrrolidine P4 Motifs also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Magnesium (Mg) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure and Property Based Design of Factor Xa Inhibitors: Pyrrolidin-2-Ones with Aminoindane and Phenylpyrrolidine P4 Motifs (pdb code 2y80). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Structure and Property Based Design of Factor Xa Inhibitors: Pyrrolidin-2-Ones with Aminoindane and Phenylpyrrolidine P4 Motifs, PDB code: 2y80:

Calcium binding site 1 out of 1 in 2y80

Go back to Calcium Binding Sites List in 2y80
Calcium binding site 1 out of 1 in the Structure and Property Based Design of Factor Xa Inhibitors: Pyrrolidin-2-Ones with Aminoindane and Phenylpyrrolidine P4 Motifs


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure and Property Based Design of Factor Xa Inhibitors: Pyrrolidin-2-Ones with Aminoindane and Phenylpyrrolidine P4 Motifs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1246

b:29.4
occ:1.00
 O A:GLN75 2.3 36.3 1.0
OD1 A:ASP70 2.3 27.1 1.0
O A:ASN72 2.3 27.4 1.0
OE2 A:GLU80 2.3 28.4 1.0
O A:HOH2025 2.5 25.8 1.0
O A:HOH2027 2.7 48.6 1.0
CD A:GLU80 3.4 31.2 1.0
C A:ASN72 3.4 26.2 1.0
CG A:ASP70 3.4 26.5 1.0
C A:GLN75 3.5 41.4 1.0
CG A:GLU80 3.8 27.3 1.0
OD2 A:ASP70 4.0 24.6 1.0
N A:ASN72 4.0 22.5 1.0
CA A:ASN72 4.2 24.1 1.0
N A:GLU77 4.2 45.9 1.0
N A:GLN75 4.3 40.2 1.0
N A:THR73 4.4 28.4 1.0
CA A:GLU76 4.4 44.7 1.0
N A:GLU76 4.4 42.6 1.0
CA A:THR73 4.4 31.6 1.0
CA A:GLN75 4.4 41.4 1.0
CB A:ASN72 4.5 23.6 1.0
OE1 A:GLU80 4.5 30.7 1.0
N A:ARG71 4.6 21.3 1.0
CB A:ASP70 4.6 21.8 1.0
CA A:ASP70 4.7 22.4 1.0
C A:THR73 4.7 33.8 1.0
C A:GLU76 4.8 45.4 1.0
CG A:GLU77 4.8 53.8 1.0
CB A:GLU77 4.9 47.7 1.0
N A:GLU74 5.0 35.9 1.0

Reference:

R.J.Young, C.Adams, M.Blows, D.Brown, C.L.Burns-Kurtis, C.Chan, L.Chaudry, M.A.Convery, D.E.Davies, A.M.Exall, G.Foster, J.D.Harling, E.Hortense, S.Irvine, W.R.Irving, S.Jackson, S.Kleanthous, A.J.Pateman, A.N.Patikis, T.J.Roethka, S.Senger, G.J.Stelman, J.R.Toomey, R.I.West, C.Whittaker, P.Zhou, N.S.Watson. Structure and Property Based Design of Factor Xa Inhibitors: Pyrrolidin-2-Ones with Aminoindane and Phenylpyrrolidine P4 Motifs. Bioorg.Med.Chem.Lett. V. 21 1582 2011.
ISSN: ISSN 0960-894X
PubMed: 21349710
DOI: 10.1016/J.BMCL.2011.01.131
Page generated: Fri Jul 12 19:25:56 2024

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