Zinc in PDB 6imi: 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: 6imi was solved by X.Zhang, H.Su, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.58 / 1.46
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.414, 80.530, 163.844, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.7

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

Magnesium

(Mg)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE4D Complexed with A Novel Inhibitor (pdb code 6imi). 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: 6imi:
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:Zn503 b:13.7 occ:1.00 OD2 A:ASP201 2.1 6.4 1.0 OD1 A:ASP318 2.1 8.2 1.0 O A:HOH618 2.1 8.1 1.0 NE2 A:HIS164 2.2 7.5 1.0 NE2 A:HIS200 2.2 6.7 1.0 O A:HOH702 2.2 7.9 1.0 CG A:ASP318 3.0 12.6 1.0 CG A:ASP201 3.1 7.2 1.0 CD2 A:HIS200 3.1 6.0 1.0 CE1 A:HIS164 3.2 7.9 1.0 CD2 A:HIS164 3.2 6.5 1.0 CE1 A:HIS200 3.2 8.8 1.0 OD2 A:ASP318 3.3 13.1 1.0 OD1 A:ASP201 3.6 6.8 1.0 MG A:MG501 3.8 7.8 1.0 O A:HOH786 3.8 8.5 1.0 O A:HOH638 4.1 16.8 1.0 O A:HOH816 4.1 33.8 1.0 CD2 A:HIS160 4.1 8.9 1.0 CB A:ASP201 4.3 6.6 1.0 ND1 A:HIS164 4.3 6.6 1.0 CG A:HIS200 4.3 6.5 1.0 CG A:HIS164 4.3 6.5 1.0 ND1 A:HIS200 4.3 7.8 1.0 NE2 A:HIS160 4.3 10.1 1.0 CB A:ASP318 4.5 7.7 1.0 O A:HOH657 4.7 7.6 1.0 CG2 A:VAL168 4.8 8.3 1.0 CA A:ASP318 5.0 7.8 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:Zn502 b:18.0 occ:1.00 OD2 B:ASP201 2.1 9.1 1.0 OD1 B:ASP318 2.1 16.5 1.0 O B:HOH615 2.1 9.1 1.0 O B:HOH674 2.2 10.5 1.0 NE2 B:HIS164 2.2 10.0 1.0 NE2 B:HIS200 2.2 10.0 1.0 CG B:ASP318 3.0 16.6 1.0 CD2 B:HIS200 3.1 9.4 1.0 CG B:ASP201 3.1 9.2 1.0 CD2 B:HIS164 3.2 11.9 1.0 CE1 B:HIS164 3.2 10.6 1.0 CE1 B:HIS200 3.2 13.3 1.0 OD2 B:ASP318 3.3 22.2 1.0 OD1 B:ASP201 3.6 8.3 1.0 MG B:MG501 3.8 9.1 1.0 O B:HOH702 3.9 10.0 1.0 O B:HOH636 4.1 19.9 1.0 CD2 B:HIS160 4.1 11.8 1.0 CG B:HIS200 4.3 10.2 1.0 ND1 B:HIS164 4.3 11.6 1.0 ND1 B:HIS200 4.3 9.7 1.0 CB B:ASP201 4.3 7.9 1.0 CG B:HIS164 4.3 12.3 1.0 O B:HOH731 4.3 32.5 1.0 NE2 B:HIS160 4.4 12.3 1.0 CB B:ASP318 4.4 16.9 1.0 O B:HOH625 4.7 8.9 1.0 CG2 B:VAL168 4.7 13.5 1.0 CA B:ASP318 4.9 17.0 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