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Zinc in PDB 3shy: Crystal Structure of the PDE5A1 Catalytic Domain in Complex with Novel Inhibitors

Enzymatic activity of Crystal Structure of the PDE5A1 Catalytic Domain in Complex with Novel Inhibitors

All present enzymatic activity of Crystal Structure of the PDE5A1 Catalytic Domain in Complex with Novel Inhibitors:
3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of the PDE5A1 Catalytic Domain in Complex with Novel Inhibitors, PDB code: 3shy was solved by T.T.Chen, T.Chen, Y.C.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.33 / 2.65
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 74.458, 74.458, 131.926, 90.00, 90.00, 120.00
R / Rfree (%) 21.1 / 25.9

Other elements in 3shy:

The structure of Crystal Structure of the PDE5A1 Catalytic Domain in Complex with Novel Inhibitors also contains other interesting chemical elements:

Fluorine (F) 1 atom
Magnesium (Mg) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the PDE5A1 Catalytic Domain in Complex with Novel Inhibitors (pdb code 3shy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of the PDE5A1 Catalytic Domain in Complex with Novel Inhibitors, PDB code: 3shy:

Zinc binding site 1 out of 1 in 3shy

Go back to Zinc Binding Sites List in 3shy
Zinc binding site 1 out of 1 in the Crystal Structure of the PDE5A1 Catalytic Domain in Complex with Novel Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the PDE5A1 Catalytic Domain in Complex with Novel Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn861

b:67.1
occ:1.00
 OD2 A:ASP654 2.2 50.6 1.0
OD1 A:ASP764 2.3 56.7 1.0
NE2 A:HIS653 2.4 45.6 1.0
NE2 A:HIS617 2.4 51.9 1.0
O A:HOH864 2.8 57.9 1.0
OD2 A:ASP764 2.9 58.1 1.0
CG A:ASP764 2.9 53.9 1.0
CD2 A:HIS653 3.1 43.7 1.0
MG A:MG862 3.2 70.1 1.0
CG A:ASP654 3.2 51.0 1.0
CD2 A:HIS617 3.3 52.1 1.0
CE1 A:HIS617 3.4 45.0 1.0
CE1 A:HIS653 3.5 49.6 1.0
OD1 A:ASP654 3.6 55.8 1.0
CD2 A:HIS613 4.0 57.4 1.0
NE2 A:HIS613 4.2 60.2 1.0
CG A:HIS653 4.3 46.4 1.0
CB A:ASP764 4.4 50.0 1.0
CB A:ASP654 4.4 46.1 1.0
ND1 A:HIS617 4.5 45.7 1.0
CG A:HIS617 4.5 49.1 1.0
ND1 A:HIS653 4.5 47.4 1.0
O A:HOH11 4.7 65.8 1.0
O A:ASP764 4.9 50.9 1.0
CA A:ASP764 5.0 48.9 1.0

Reference:

Z.Xu, Z.Liu, T.Chen, T.T.Chen, Z.Wang, G.Tian, J.Shi, X.Wang, Y.Lu, X.Yan, G.Wang, H.Jiang, K.Chen, S.Wang, Y.Xu, J.Shen, W.Zhu. Utilization of Halogen Bond in Lead Optimization: A Case Study of Rational Design of Potent Phosphodiesterase Type 5 (PDE5) Inhibitors. J.Med.Chem. V. 54 5607 2011.
ISSN: ISSN 0022-2623
PubMed: 21714539
DOI: 10.1021/JM200644R
Page generated: Wed Aug 20 14:02:37 2025

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