Sodium in PDB 8bpy: X-Ray Structure of PDE9A in Complex with Inhibitor 13A

Enzymatic activity of X-Ray Structure of PDE9A in Complex with Inhibitor 13A

All present enzymatic activity of X-Ray Structure of PDE9A in Complex with Inhibitor 13A:
3.1.4.35;

Protein crystallography data

The structure of X-Ray Structure of PDE9A in Complex with Inhibitor 13A, PDB code: 8bpy was solved by H.Steuber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.74 / 3.30
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 222.423, 222.423, 120.257, 90, 90, 90
R / Rfree (%) 24.6 / 31.2

Other elements in 8bpy:

The structure of X-Ray Structure of PDE9A in Complex with Inhibitor 13A also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of PDE9A in Complex with Inhibitor 13A (pdb code 8bpy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure of PDE9A in Complex with Inhibitor 13A, PDB code: 8bpy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8bpy

Go back to Sodium Binding Sites List in 8bpy
Sodium binding site 1 out of 2 in the X-Ray Structure of PDE9A in Complex with Inhibitor 13A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of PDE9A in Complex with Inhibitor 13A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2003

b:30.9
occ:0.00
O A:ASP244 2.3 99.6 1.0
O A:TYR246 2.7 100.0 1.0
C A:ASP244 3.5 90.9 1.0
C A:TYR246 3.8 90.8 1.0
CA A:ASP244 4.3 96.9 1.0
O A:HIS243 4.3 89.7 1.0
CA A:ARG247 4.4 100.3 1.0
N A:ASN245 4.4 86.7 1.0
N A:ARG247 4.5 99.8 1.0
N A:TYR246 4.6 86.9 1.0
CA A:ASN245 4.7 83.7 1.0
C A:ASN245 4.7 83.6 1.0
CA A:TYR246 4.9 80.6 1.0

Sodium binding site 2 out of 2 in 8bpy

Go back to Sodium Binding Sites List in 8bpy
Sodium binding site 2 out of 2 in the X-Ray Structure of PDE9A in Complex with Inhibitor 13A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of PDE9A in Complex with Inhibitor 13A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2003

b:76.9
occ:0.00
O B:ASP244 2.1 167.8 1.0
O B:TYR246 2.2 143.7 1.0
C B:ASP244 3.0 189.2 1.0
C B:TYR246 3.4 153.3 1.0
CA B:ASP244 3.7 182.1 1.0
O B:HIS243 3.8 148.3 1.0
N B:TYR246 3.9 164.2 1.0
N B:ASN245 4.0 200.5 1.0
OD1 B:ASP244 4.1 174.8 1.0
CA B:ASN245 4.3 187.6 1.0
N B:ARG247 4.3 159.3 1.0
CA B:ARG247 4.4 174.1 1.0
CA B:TYR246 4.4 155.6 1.0
C B:ASN245 4.6 166.2 1.0
CG B:ASP244 4.7 190.8 1.0
C B:HIS243 4.7 156.9 1.0
N B:ASP244 4.7 164.5 1.0
CB B:ASP244 4.8 187.8 1.0

Reference:

D.Meibom, S.Micus, A.L.Andreevski, S.Anlauf, P.Bogner, C.J.Von Buehler, A.P.Dieskau, J.Dreher, F.Eitner, D.Fliegner, M.Follmann, K.M.Gericke, S.Maassen, J.Meyer, K.H.Schlemmer, H.Steuber, A.Tersteegen, F.Wunder. Bay-7081: A Potent, Selective, and Orally Bioavailable Cyanopyridone-Based PDE9A Inhibitor. J.Med.Chem. V. 65 16420 2022.
ISSN: ISSN 0022-2623
PubMed: 36475653
DOI: 10.1021/ACS.JMEDCHEM.2C01267
Page generated: Fri Apr 7 17:59:30 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy