Zinc in PDB 6l6e: Human PDE5 Catalytic Core in Complex with Avanafil

All present enzymatic activity of Human PDE5 Catalytic Core in Complex with Avanafil:
3.1.4.35;

The structure of Human PDE5 Catalytic Core in Complex with Avanafil, PDB code: 6l6e was solved by C.M.Hsieh, N.L.Chan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.57 / 1.92
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	75.837, 75.837, 160.610, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 20.7

The structure of Human PDE5 Catalytic Core in Complex with Avanafil also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Human PDE5 Catalytic Core in Complex with Avanafil (pdb code 6l6e). 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 Human PDE5 Catalytic Core in Complex with Avanafil, PDB code: 6l6e:

Zinc binding site 1 out of 1 in the Human PDE5 Catalytic Core in Complex with Avanafil


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human PDE5 Catalytic Core in Complex with Avanafil within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:21.5 occ:0.64 O A:HOH1032 2.0 22.0 1.0 OD1 A:ASP764 2.1 21.6 1.0 OD2 A:ASP654 2.2 24.0 1.0 O2 A:SO4904 2.3 28.7 1.0 NE2 A:HIS653 2.3 20.5 1.0 NE2 A:HIS617 2.3 28.5 1.0 CG A:ASP764 2.9 28.7 1.0 CD2 A:HIS653 3.1 21.5 1.0 OD2 A:ASP764 3.1 32.5 1.0 CD2 A:HIS617 3.1 22.6 1.0 CG A:ASP654 3.2 27.0 1.0 CE1 A:HIS653 3.4 21.5 1.0 CE1 A:HIS617 3.4 23.5 1.0 S A:SO4904 3.5 27.9 1.0 MG A:MG903 3.7 23.3 1.0 OD1 A:ASP654 3.7 23.9 1.0 O A:HOH1052 3.8 25.4 1.0 O3 A:SO4904 3.9 42.3 1.0 O4 A:SO4904 3.9 42.5 1.0 CD2 A:HIS613 4.1 28.5 1.0 CG A:HIS653 4.3 21.6 1.0 CB A:ASP764 4.4 19.4 1.0 CG A:HIS617 4.4 23.0 1.0 ND1 A:HIS653 4.4 22.0 1.0 ND1 A:HIS617 4.5 22.1 1.0 CB A:ASP654 4.5 19.7 1.0 NE2 A:HIS613 4.5 26.8 1.0 O1 A:SO4904 4.6 42.4 1.0 O A:HOH1020 4.7 21.0 1.0 CA A:ASP764 4.9 20.2 1.0 O A:ASP764 4.9 23.4 1.0

C.M.Hsieh, C.Y.Chen, J.W.Chern, N.L.Chan. Structure of Human Phosphodiesterase 5A1 Complexed with Avanafil Reveals Molecular Basis of Isoform Selectivity and Guidelines For Targeting Alpha-Helix Backbone Oxygen By Halogen Bonding. J.Med.Chem. V. 63 8485 2020.
ISSN: ISSN 0022-2623
PubMed: 32663396
DOI: 10.1021/ACS.JMEDCHEM.0C00853