Zinc in PDB 6imb: 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: 6imb 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)	36.45 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.497, 80.432, 163.532, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 21.9

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

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE4D Complexed with A Novel Inhibitor (pdb code 6imb). 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: 6imb:
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:11.3 occ:1.00 OD2 A:ASP201 2.1 5.4 1.0 O A:HOH611 2.1 7.0 1.0 O A:HOH725 2.1 8.2 1.0 OD1 A:ASP318 2.1 6.1 1.0 NE2 A:HIS200 2.2 4.3 1.0 NE2 A:HIS164 2.2 6.4 1.0 CG A:ASP318 3.1 10.4 1.0 CG A:ASP201 3.1 4.8 1.0 CD2 A:HIS200 3.1 4.8 1.0 CD2 A:HIS164 3.2 5.9 1.0 CE1 A:HIS164 3.2 5.3 1.0 CE1 A:HIS200 3.2 6.2 1.0 OD2 A:ASP318 3.3 12.8 1.0 OD1 A:ASP201 3.6 5.6 1.0 MG A:MG502 3.7 7.2 1.0 O A:HOH753 3.7 8.0 1.0 O A:HOH649 4.1 16.9 1.0 O A:HOH804 4.1 18.1 1.0 CD2 A:HIS160 4.1 8.2 1.0 CB A:ASP201 4.3 5.7 1.0 CG A:HIS200 4.3 4.8 1.0 ND1 A:HIS200 4.3 6.2 1.0 ND1 A:HIS164 4.3 5.9 1.0 CG A:HIS164 4.3 5.3 1.0 NE2 A:HIS160 4.4 11.1 1.0 CB A:ASP318 4.4 6.8 1.0 O A:HOH661 4.7 6.5 1.0 CG2 A:VAL168 4.8 7.1 1.0 CA A:ASP318 5.0 5.9 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:13.7 occ:1.00 OD2 B:ASP201 2.1 7.5 1.0 O B:HOH625 2.1 9.0 1.0 OD1 B:ASP318 2.1 9.5 1.0 NE2 B:HIS200 2.2 7.4 1.0 NE2 B:HIS164 2.2 8.8 1.0 O B:HOH696 2.2 10.6 1.0 CD2 B:HIS200 3.1 9.1 1.0 CG B:ASP318 3.1 13.4 1.0 CG B:ASP201 3.1 7.2 1.0 CD2 B:HIS164 3.2 8.9 1.0 CE1 B:HIS164 3.2 10.4 1.0 CE1 B:HIS200 3.2 9.2 1.0 OD2 B:ASP318 3.3 15.0 1.0 OD1 B:ASP201 3.6 7.5 1.0 MG B:MG503 3.7 7.3 1.0 O B:HOH738 3.8 9.0 1.0 O B:HOH669 4.0 19.4 1.0 CD2 B:HIS160 4.1 8.8 1.0 O B:HOH759 4.2 22.7 1.0 CG B:HIS200 4.2 8.7 1.0 ND1 B:HIS200 4.3 8.3 1.0 ND1 B:HIS164 4.3 9.1 1.0 CB B:ASP201 4.3 8.0 1.0 CG B:HIS164 4.3 10.5 1.0 NE2 B:HIS160 4.4 11.8 1.0 CB B:ASP318 4.5 11.2 1.0 O B:HOH640 4.7 8.6 1.0 CG2 B:VAL168 4.7 12.7 1.0 CA B:ASP318 5.0 11.2 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