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Sodium in PDB 5tnt: Discovery of Novel Aminobenzisoxazole Derivatives As Orally Available Factor Ixa Inhibitors

Enzymatic activity of Discovery of Novel Aminobenzisoxazole Derivatives As Orally Available Factor Ixa Inhibitors

All present enzymatic activity of Discovery of Novel Aminobenzisoxazole Derivatives As Orally Available Factor Ixa Inhibitors:
3.4.21.22;

Protein crystallography data

The structure of Discovery of Novel Aminobenzisoxazole Derivatives As Orally Available Factor Ixa Inhibitors, PDB code: 5tnt was solved by I.Sakurada, T.Endo, K.Hikita, T.Hirabayashi, Y.Hosaka, Y.Kato, Y.Maeda, S.Matsumoto, T.Mizuno, A.Nagasue, T.Nishimura, S.Shimada, M.Shinozaki, K.Taguchi, K.Takeuchi, T.Yokoyama, A.Hruza, P.Reichert, T.Zhang, H.B.Wood, K.Nakao, S.Furusako, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.50 / 1.40
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 99.084, 99.084, 94.680, 90.00, 90.00, 120.00
R / Rfree (%) 14.6 / 16.1

Other elements in 5tnt:

The structure of Discovery of Novel Aminobenzisoxazole Derivatives As Orally Available Factor Ixa Inhibitors also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Discovery of Novel Aminobenzisoxazole Derivatives As Orally Available Factor Ixa Inhibitors (pdb code 5tnt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Discovery of Novel Aminobenzisoxazole Derivatives As Orally Available Factor Ixa Inhibitors, PDB code: 5tnt:

Sodium binding site 1 out of 1 in 5tnt

Go back to Sodium Binding Sites List in 5tnt
Sodium binding site 1 out of 1 in the Discovery of Novel Aminobenzisoxazole Derivatives As Orally Available Factor Ixa Inhibitors


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Discovery of Novel Aminobenzisoxazole Derivatives As Orally Available Factor Ixa Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:18.7
occ:1.00
O A:GLU75 2.2 25.5 1.0
OE1 A:GLU70 2.3 14.9 1.0
O A:ASN72 2.3 18.8 1.0
O A:HOH441 2.4 18.9 1.0
OE2 A:GLU80 2.4 24.4 1.0
O A:HOH402 2.7 27.6 1.0
H A:ASN72 3.2 15.3 1.0
CD A:GLU70 3.2 15.1 1.0
C A:ASN72 3.3 18.7 1.0
HG3 A:GLU77 3.4 47.0 1.0
CD A:GLU80 3.4 30.2 1.0
H A:GLU77 3.4 28.0 1.0
C A:GLU75 3.4 28.4 1.0
H A:HIS71 3.4 11.8 1.0
H A:GLU75 3.4 24.4 1.0
OE2 A:GLU70 3.5 19.5 1.0
HA A:ILE73 3.7 21.6 1.0
HG2 A:GLU80 3.7 19.9 1.0
HA A:THR76 3.8 29.7 1.0
HB2 A:GLU77 3.8 29.6 1.0
N A:ASN72 3.9 15.2 1.0
HB3 A:ASN72 3.9 18.1 1.0
HB2 A:GLU75 4.0 25.9 1.0
CG A:GLU80 4.0 17.2 1.0
N A:GLU77 4.1 29.0 1.0
O A:HOH561 4.1 26.3 1.0
CA A:ASN72 4.1 16.1 1.0
HG3 A:GLU80 4.2 17.4 1.0
CG A:GLU77 4.2 47.0 1.0
N A:GLU75 4.2 23.9 1.0
HA A:GLU70 4.2 12.0 1.0
N A:ILE73 4.3 17.6 1.0
CA A:GLU75 4.3 24.0 1.0
OE1 A:GLU80 4.3 28.1 1.0
N A:THR76 4.4 30.0 1.0
CA A:ILE73 4.4 19.3 1.0
CA A:THR76 4.4 30.4 1.0
CB A:GLU77 4.4 30.5 1.0
O A:HOH436 4.4 60.1 1.0
N A:HIS71 4.4 13.2 1.0
O A:HOH497 4.5 40.9 1.0
CG A:GLU70 4.6 15.7 1.0
CD A:GLU77 4.6 76.7 1.0
CB A:ASN72 4.6 16.6 1.0
C A:THR76 4.6 35.0 1.0
HG3 A:GLU70 4.6 15.7 1.0
CB A:GLU75 4.7 25.7 1.0
HB3 A:HIS71 4.7 14.3 1.0
C A:ILE73 4.7 24.1 1.0
OE1 A:GLU77 4.8 88.7 1.0
C A:HIS71 4.8 16.5 1.0
CA A:GLU77 4.9 28.0 1.0

Reference:

I.Sakurada, T.Endo, K.Hikita, T.Hirabayashi, Y.Hosaka, Y.Kato, Y.Maeda, S.Matsumoto, T.Mizuno, H.Nagasue, T.Nishimura, S.Shimada, M.Shinozaki, K.Taguchi, K.Takeuchi, T.Yokoyama, A.Hruza, P.Reichert, T.Zhang, H.B.Wood, K.Nakao, S.Furusako. Discovery of Novel Aminobenzisoxazole Derivatives As Orally Available Factor Ixa Inhibitors. Bioorg. Med. Chem. Lett. V. 27 2622 2017.
ISSN: ESSN 1464-3405
PubMed: 28408226
DOI: 10.1016/J.BMCL.2017.03.002
Page generated: Tue Dec 15 11:37:56 2020

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