Zinc in PDB 6imt: 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: 6imt 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)	30.91 / 1.48
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.125, 80.599, 163.785, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 19.6

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

Fluorine	(F)	2 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE4D Complexed with A Novel Inhibitor (pdb code 6imt). 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: 6imt:
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:13.7 occ:1.00 OD2 A:ASP201 2.0 6.4 1.0 O A:HOH620 2.1 8.7 1.0 OD1 A:ASP318 2.1 6.8 1.0 O A:HOH707 2.2 8.1 1.0 NE2 A:HIS164 2.2 6.7 1.0 NE2 A:HIS200 2.2 6.6 1.0 CG A:ASP201 3.1 5.8 1.0 CG A:ASP318 3.1 9.8 1.0 CD2 A:HIS200 3.1 6.5 1.0 CE1 A:HIS164 3.2 7.0 1.0 CD2 A:HIS164 3.2 6.3 1.0 CE1 A:HIS200 3.2 7.5 1.0 OD2 A:ASP318 3.3 14.9 1.0 OD1 A:ASP201 3.6 6.7 1.0 MG A:MG502 3.8 7.8 1.0 O A:HOH773 3.9 8.1 1.0 O A:HOH643 4.0 12.3 1.0 CD2 A:HIS160 4.1 8.6 1.0 CB A:ASP201 4.3 6.5 1.0 CG A:HIS200 4.3 6.9 1.0 ND1 A:HIS164 4.3 6.4 1.0 O A:HOH813 4.3 26.8 1.0 ND1 A:HIS200 4.3 6.5 1.0 NE2 A:HIS160 4.3 11.3 1.0 CG A:HIS164 4.3 5.9 1.0 CB A:ASP318 4.5 7.5 1.0 O A:HOH655 4.7 8.1 1.0 CG2 A:VAL168 4.7 8.4 1.0 CA A:ASP318 5.0 7.4 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:16.7 occ:1.00 OD2 B:ASP201 2.1 9.2 1.0 O B:HOH615 2.1 9.9 1.0 OD1 B:ASP318 2.1 14.7 1.0 O B:HOH688 2.2 10.6 1.0 NE2 B:HIS164 2.2 10.9 1.0 NE2 B:HIS200 2.2 8.4 1.0 CG B:ASP318 3.1 15.9 1.0 CD2 B:HIS200 3.1 8.9 1.0 CG B:ASP201 3.1 8.2 1.0 CD2 B:HIS164 3.1 11.8 1.0 CE1 B:HIS164 3.2 10.6 1.0 CE1 B:HIS200 3.2 10.5 1.0 OD2 B:ASP318 3.3 20.3 1.0 OD1 B:ASP201 3.6 8.2 1.0 MG B:MG502 3.7 8.6 1.0 O B:HOH721 3.9 10.2 1.0 O B:HOH634 4.0 16.8 1.0 CD2 B:HIS160 4.1 11.5 1.0 CG B:HIS200 4.3 9.4 1.0 ND1 B:HIS164 4.3 12.5 1.0 ND1 B:HIS200 4.3 9.6 1.0 CG B:HIS164 4.3 11.3 1.0 CB B:ASP201 4.3 8.4 1.0 NE2 B:HIS160 4.3 13.1 1.0 O B:HOH739 4.4 30.4 1.0 CB B:ASP318 4.5 15.3 1.0 O B:HOH631 4.7 9.4 1.0 CG2 B:VAL168 4.7 13.7 1.0 CA B:ASP318 5.0 15.3 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