Zinc in PDB 7cbq: Crystal Structure of PDE4D Catalytic Domain in Complex with Apremilast

All present enzymatic activity of Crystal Structure of PDE4D Catalytic Domain in Complex with Apremilast:
3.1.4.53;

The structure of Crystal Structure of PDE4D Catalytic Domain in Complex with Apremilast, PDB code: 7cbq was solved by X.L.Zhang, Y.C.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.07 / 1.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.787, 80.221, 163.468, 90, 90, 90
R / Rfree (%)	17.6 / 20.5

The structure of Crystal Structure of PDE4D Catalytic Domain in Complex with Apremilast also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE4D Catalytic Domain in Complex with Apremilast (pdb code 7cbq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of PDE4D Catalytic Domain in Complex with Apremilast, PDB code: 7cbq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of PDE4D Catalytic Domain in Complex with Apremilast


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 PDE4D Catalytic Domain in Complex with Apremilast within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:11.4 occ:1.00 OD2 A:ASP201 2.0 6.4 1.0 OD1 A:ASP318 2.1 6.1 1.0 O A:HOH652 2.1 6.3 1.0 NE2 A:HIS164 2.2 6.7 1.0 NE2 A:HIS200 2.2 6.0 1.0 O A:HOH630 2.2 6.8 1.0 CG A:ASP318 3.0 7.8 1.0 CG A:ASP201 3.1 7.3 1.0 CD2 A:HIS200 3.1 6.2 1.0 CE1 A:HIS164 3.1 6.8 1.0 CD2 A:HIS164 3.2 6.2 1.0 CE1 A:HIS200 3.2 7.2 1.0 OD2 A:ASP318 3.3 10.4 1.0 OD1 A:ASP201 3.6 5.3 1.0 MG A:MG501 3.8 6.0 1.0 O A:HOH758 3.9 6.6 1.0 O A:HOH694 4.1 7.2 1.0 CD2 A:HIS160 4.1 7.3 1.0 NE2 A:HIS160 4.2 8.3 1.0 ND1 A:HIS164 4.3 6.0 1.0 CB A:ASP201 4.3 5.2 1.0 CG A:HIS200 4.3 4.2 1.0 ND1 A:HIS200 4.3 6.2 1.0 CG A:HIS164 4.3 4.4 1.0 CB A:ASP318 4.4 5.3 1.0 C14 A:A9L511 4.7 17.3 1.0 CG2 A:VAL168 4.7 7.2 1.0 O A:HOH661 4.7 5.8 1.0 CA A:ASP318 4.9 5.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE4D Catalytic Domain in Complex with Apremilast


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of PDE4D Catalytic Domain in Complex with Apremilast within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:14.1 occ:1.00 OD2 B:ASP201 2.1 8.3 1.0 OD1 B:ASP318 2.1 9.1 1.0 O B:HOH654 2.1 9.6 1.0 NE2 B:HIS164 2.2 9.2 1.0 NE2 B:HIS200 2.2 8.6 1.0 O B:HOH613 2.2 8.8 1.0 CG B:ASP318 3.1 12.6 1.0 CD2 B:HIS200 3.1 8.3 1.0 CE1 B:HIS164 3.1 9.8 1.0 CG B:ASP201 3.1 8.1 1.0 CD2 B:HIS164 3.1 10.7 1.0 CE1 B:HIS200 3.2 8.9 1.0 OD2 B:ASP318 3.4 13.7 1.0 OD1 B:ASP201 3.6 7.8 1.0 MG B:MG502 3.8 7.7 1.0 O B:HOH727 4.0 8.3 1.0 CD2 B:HIS160 4.1 8.8 1.0 O B:HOH649 4.1 12.0 1.0 NE2 B:HIS160 4.2 9.8 1.0 ND1 B:HIS164 4.2 11.9 1.0 CG B:HIS200 4.3 8.4 1.0 CG B:HIS164 4.3 10.6 1.0 ND1 B:HIS200 4.3 8.8 1.0 CB B:ASP201 4.3 8.3 1.0 CB B:ASP318 4.4 9.6 1.0 C14 B:A9L507 4.7 20.7 1.0 CG2 B:VAL168 4.7 10.4 1.0 O B:HOH623 4.8 7.5 1.0 CA B:ASP318 4.9 10.0 1.0

R.Zhang, H.Li, X.Zhang, J.Li, H.Su, Q.Lu, G.Dong, H.Dou, C.Fan, Z.Gu, Q.Mu, W.Tang, Y.Xu, H.Liu. Design, Synthesis, and Biological Evaluation of Tetrahydroisoquinolines Derivatives As Novel, Selective PDE4 Inhibitors For Antipsoriasis Treatment. Eur.J.Med.Chem. 13004 2020.
ISSN: ISSN 0223-5234
PubMed: 33218684
DOI: 10.1016/J.EJMECH.2020.113004