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Zinc in PDB 5zz2: Crystal Structure of PDE5 in Complex with Inhibitor LW1634

Enzymatic activity of Crystal Structure of PDE5 in Complex with Inhibitor LW1634

All present enzymatic activity of Crystal Structure of PDE5 in Complex with Inhibitor LW1634:
3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of PDE5 in Complex with Inhibitor LW1634, PDB code: 5zz2 was solved by D.Wu, Y.D.Huang, Y.Y.Huang, H.B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.73 / 2.60
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 74.474, 74.474, 132.341, 90.00, 90.00, 120.00
R / Rfree (%) 20.9 / 26.4

Other elements in 5zz2:

The structure of Crystal Structure of PDE5 in Complex with Inhibitor LW1634 also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of PDE5 in Complex with Inhibitor LW1634 (pdb code 5zz2). 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 PDE5 in Complex with Inhibitor LW1634, PDB code: 5zz2:

Zinc binding site 1 out of 1 in 5zz2

Go back to Zinc Binding Sites List in 5zz2
Zinc binding site 1 out of 1 in the Crystal Structure of PDE5 in Complex with Inhibitor LW1634


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 PDE5 in Complex with Inhibitor LW1634 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:44.2
occ:1.00
O3 A:SO4903 1.6 39.2 1.0
OD2 A:ASP654 2.0 33.8 1.0
OD1 A:ASP764 2.1 34.1 1.0
NE2 A:HIS653 2.2 33.7 1.0
NE2 A:HIS617 2.2 35.0 1.0
O A:HOH1008 2.4 27.4 1.0
CG A:ASP764 3.0 32.2 1.0
S A:SO4903 3.0 32.2 1.0
CE1 A:HIS617 3.1 32.4 1.0
CE1 A:HIS653 3.1 32.4 1.0
CD2 A:HIS653 3.2 31.9 1.0
CG A:ASP654 3.2 31.8 1.0
CD2 A:HIS617 3.2 32.0 1.0
OD2 A:ASP764 3.3 34.5 1.0
O A:HOH1022 3.6 21.2 1.0
O2 A:SO4903 3.7 34.7 1.0
O4 A:SO4903 3.7 35.0 1.0
OD1 A:ASP654 3.7 31.9 1.0
MG A:MG902 3.7 29.3 1.0
O1 A:SO4903 4.1 32.7 1.0
CD2 A:HIS613 4.2 32.7 1.0
ND1 A:HIS653 4.3 31.1 1.0
ND1 A:HIS617 4.3 31.7 1.0
CG A:HIS653 4.3 30.9 1.0
CG A:HIS617 4.3 30.9 1.0
CB A:ASP764 4.4 32.0 1.0
CB A:ASP654 4.4 31.0 1.0
NE2 A:HIS613 4.6 32.1 1.0
O A:HOH1004 4.6 23.0 1.0
O A:ASP764 4.8 33.6 1.0
CA A:ASP764 4.9 31.8 1.0

Reference:

D.Wu, Y.Huang, Y.Chen, Y.Y.Huang, H.Geng, T.Zhang, C.Zhang, Z.Li, L.Guo, J.Chen, H.B.Luo. Optimization of Chromeno[2,3- C]Pyrrol-9(2 H)-Ones As Highly Potent, Selective, and Orally Bioavailable PDE5 Inhibitors: Structure-Activity Relationship, X-Ray Crystal Structure, and Pharmacodynamic Effect on Pulmonary Arterial Hypertension. J. Med. Chem. V. 61 8468 2018.
ISSN: ISSN 1520-4804
PubMed: 30148362
DOI: 10.1021/ACS.JMEDCHEM.8B01209
Page generated: Wed Dec 16 11:28:21 2020

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