Zinc in PDB 5k32: PDE4D Crystal Structure in Complex with Small Molecule Inhibitor

All present enzymatic activity of PDE4D Crystal Structure in Complex with Small Molecule Inhibitor:
3.1.4.53;

The structure of PDE4D Crystal Structure in Complex with Small Molecule Inhibitor, PDB code: 5k32 was solved by V.Segarra, B.Hernandez, R.Roberts, J.Gracia, M.Soler, I.Bonin, J.Aymami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.967, 79.739, 163.845, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 28.1

The structure of PDE4D Crystal Structure in Complex with Small Molecule Inhibitor also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the PDE4D Crystal Structure in Complex with Small Molecule Inhibitor (pdb code 5k32). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the PDE4D Crystal Structure in Complex with Small Molecule Inhibitor, PDB code: 5k32:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the PDE4D Crystal Structure in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PDE4D Crystal Structure in Complex with Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:26.9 occ:1.00 OD2 A:ASP201 2.1 15.0 1.0 O A:HOH1154 2.2 22.1 1.0 NE2 A:HIS164 2.2 10.5 1.0 O A:HOH1214 2.2 21.6 1.0 NE2 A:HIS200 2.3 14.9 1.0 OD1 A:ASP318 2.4 18.5 1.0 CG A:ASP201 3.1 20.0 1.0 CD2 A:HIS200 3.1 17.2 1.0 CE1 A:HIS164 3.2 11.7 1.0 CD2 A:HIS164 3.2 12.3 1.0 CG A:ASP318 3.2 13.3 1.0 OD2 A:ASP318 3.4 19.9 1.0 CE1 A:HIS200 3.4 21.9 1.0 OD1 A:ASP201 3.5 20.3 1.0 MG A:MG1002 3.6 18.4 1.0 O A:HOH1218 3.7 17.6 1.0 CD2 A:HIS160 4.0 16.9 1.0 O A:HOH1150 4.1 22.4 1.0 NE2 A:HIS160 4.2 18.6 1.0 CB A:ASP201 4.3 17.1 1.0 ND1 A:HIS164 4.3 17.6 1.0 CG A:HIS200 4.3 19.0 1.0 CG A:HIS164 4.4 18.0 1.0 ND1 A:HIS200 4.4 15.3 1.0 CB A:ASP318 4.6 17.7 1.0 C26 A:6Q21003 4.6 27.3 1.0 O A:HOH1141 4.7 14.7 1.0 CG2 A:VAL168 4.9 17.7 1.0

Zinc binding site 2 out of 2 in the PDE4D Crystal Structure in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of PDE4D Crystal Structure in Complex with Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:24.7 occ:1.00 O B:HOH1150 2.1 17.6 1.0 OD1 B:ASP318 2.1 15.6 1.0 O B:HOH1186 2.2 14.2 1.0 OD2 B:ASP201 2.3 15.3 1.0 NE2 B:HIS164 2.3 12.9 1.0 NE2 B:HIS200 2.3 19.4 1.0 CG B:ASP318 3.1 21.5 1.0 CD2 B:HIS200 3.1 9.8 1.0 CG B:ASP201 3.2 17.0 1.0 CE1 B:HIS164 3.2 14.8 1.0 CD2 B:HIS164 3.3 13.8 1.0 OD2 B:ASP318 3.3 21.1 1.0 CE1 B:HIS200 3.4 19.6 1.0 MG B:MG1002 3.6 17.0 1.0 OD1 B:ASP201 3.7 16.1 1.0 O B:HOH1238 3.9 17.5 1.0 CD2 B:HIS160 4.1 23.6 1.0 O B:HOH1177 4.1 21.1 1.0 NE2 B:HIS160 4.2 22.2 1.0 CB B:ASP201 4.3 17.6 1.0 CG B:HIS200 4.3 15.3 1.0 ND1 B:HIS164 4.3 17.2 1.0 CG B:HIS164 4.4 15.6 1.0 ND1 B:HIS200 4.4 16.4 1.0 CB B:ASP318 4.5 17.6 1.0 C26 B:6Q21003 4.6 21.4 1.0 O B:HOH1178 4.9 17.0 1.0 CG2 B:VAL168 4.9 16.2 1.0

R.S.Roberts, S.Sevilla, M.Ferrer, J.Taltavull, B.Hernandez, V.Segarra, J.Gracia, M.D.Lehner, A.Gavalda, M.Andres, J.Cabedo, D.Vilella, P.Eichhorn, E.Calama, C.Carcasona, M.Miralpeix. 4-Amino-7,8-Dihydro-1,6-Naphthyridin-5(6 H)-Ones As Inhaled Phosphodiesterase Type 4 (PDE4) Inhibitors: Structural Biology and Structure-Activity Relationships. J. Med. Chem. V. 61 2472 2018.
ISSN: ISSN 1520-4804
PubMed: 29502405
DOI: 10.1021/ACS.JMEDCHEM.7B01751