Zinc in PDB 6inm: Crystal Structure of PDE4D Complexed with A Novel Inhibitor

All present enzymatic activity of Crystal Structure of PDE4D Complexed with A Novel Inhibitor:
3.1.4.53;

The structure of Crystal Structure of PDE4D Complexed with A Novel Inhibitor, PDB code: 6inm was solved by X.L.Zhang, H.X.Su, Y.C.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.01 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.122, 80.104, 163.259, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22.4

The structure of Crystal Structure of PDE4D Complexed with A Novel Inhibitor also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE4D Complexed with A Novel Inhibitor (pdb code 6inm). 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 Complexed with A Novel Inhibitor, PDB code: 6inm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of PDE4D Complexed with A Novel Inhibitor


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 Complexed with A Novel Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:23.9 occ:1.00 OD2 A:ASP201 2.1 21.8 1.0 OD1 A:ASP318 2.1 21.5 1.0 NE2 A:HIS164 2.2 18.0 1.0 O A:HOH618 2.2 18.2 1.0 NE2 A:HIS200 2.2 17.5 1.0 O A:HOH691 2.2 18.5 1.0 CG A:ASP318 3.0 25.2 1.0 CD2 A:HIS200 3.0 16.8 1.0 CG A:ASP201 3.1 22.8 1.0 CD2 A:HIS164 3.1 18.6 1.0 CE1 A:HIS164 3.2 20.8 1.0 OD2 A:ASP318 3.2 24.7 1.0 CE1 A:HIS200 3.3 18.0 1.0 OD1 A:ASP201 3.6 21.6 1.0 MG A:MG502 3.6 18.0 1.0 O A:HOH714 3.7 19.3 1.0 O A:HOH644 3.9 36.1 1.0 CD2 A:HIS160 4.2 17.5 1.0 CG A:HIS200 4.3 22.9 1.0 CB A:ASP201 4.3 21.3 1.0 ND1 A:HIS164 4.3 19.1 1.0 O A:HOH727 4.3 46.7 1.0 CG A:HIS164 4.3 20.1 1.0 ND1 A:HIS200 4.3 19.7 1.0 CB A:ASP318 4.4 21.8 1.0 NE2 A:HIS160 4.5 18.6 1.0 O A:HOH632 4.7 21.1 1.0 CG2 A:VAL168 4.8 19.1 1.0 CA A:ASP318 5.0 21.1 1.0 O A:ASP318 5.0 19.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE4D Complexed with A Novel Inhibitor


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 Complexed with A Novel Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:29.4 occ:1.00 OD2 B:ASP201 2.0 26.1 1.0 OD2 B:ASP318 2.2 32.0 1.0 O B:HOH611 2.2 22.7 1.0 O B:HOH657 2.2 26.0 1.0 NE2 B:HIS200 2.3 19.3 1.0 NE2 B:HIS164 2.3 23.5 1.0 CG B:ASP318 3.0 34.3 1.0 CG B:ASP201 3.1 25.6 1.0 CD2 B:HIS200 3.1 19.7 1.0 CD2 B:HIS164 3.2 23.8 1.0 OD1 B:ASP318 3.2 37.0 1.0 CE1 B:HIS164 3.3 25.5 1.0 CE1 B:HIS200 3.3 22.7 1.0 OD1 B:ASP201 3.5 25.7 1.0 MG B:MG502 3.7 22.2 1.0 O B:HOH660 3.7 23.2 1.0 CD2 B:HIS160 4.2 22.0 1.0 O B:HOH650 4.2 43.9 1.0 CG B:HIS200 4.3 21.8 1.0 CB B:ASP201 4.3 22.5 1.0 CG B:HIS164 4.4 24.7 1.0 ND1 B:HIS200 4.4 21.7 1.0 ND1 B:HIS164 4.4 27.2 1.0 CB B:ASP318 4.4 26.8 1.0 NE2 B:HIS160 4.5 20.5 1.0 O B:HOH610 4.7 20.6 1.0 CG2 B:VAL168 4.7 26.3 1.0 CA B:ASP318 5.0 26.9 1.0

X.Zhang, G.Dong, H.Li, W.Chen, J.Li, C.Feng, Z.Gu, F.Zhu, R.Zhang, M.Li, W.Tang, H.Liu, Y.Xu. Structure-Aided Identification and Optimization of Tetrahydro-Isoquinolines As Novel PDE4 Inhibitors Leading to Discovery of An Effective Antipsoriasis Agent. J.Med.Chem. V. 62 5579 2019.
ISSN: ISSN 0022-2623
PubMed: 31099559
DOI: 10.1021/ACS.JMEDCHEM.9B00518