Zinc in PDB 6imr: 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: 6imr 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)	30.90 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.120, 80.624, 163.669, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 23.7

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 6imr). 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: 6imr:
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:12.0 occ:1.00 OD2 A:ASP201 2.1 4.0 1.0 O A:HOH612 2.1 5.8 1.0 O A:HOH788 2.1 7.1 1.0 OD1 A:ASP318 2.1 5.0 1.0 NE2 A:HIS164 2.2 5.2 1.0 NE2 A:HIS200 2.2 4.5 1.0 CG A:ASP318 3.1 7.2 1.0 CG A:ASP201 3.1 3.3 1.0 CD2 A:HIS200 3.1 5.1 1.0 CE1 A:HIS164 3.2 4.8 1.0 CD2 A:HIS164 3.2 5.2 1.0 CE1 A:HIS200 3.3 4.6 1.0 OD2 A:ASP318 3.3 9.3 1.0 OD1 A:ASP201 3.6 4.8 1.0 O A:HOH803 3.7 7.3 1.0 MG A:MG502 3.8 5.5 1.0 O A:HOH811 3.8 13.7 1.0 O A:HOH630 4.0 19.6 1.0 CD2 A:HIS160 4.2 6.7 1.0 CB A:ASP201 4.3 4.5 1.0 CG A:HIS200 4.3 4.9 1.0 ND1 A:HIS164 4.3 5.4 1.0 CG A:HIS164 4.3 4.5 1.0 ND1 A:HIS200 4.3 4.8 1.0 CB A:ASP318 4.5 6.9 1.0 NE2 A:HIS160 4.5 9.2 1.0 O A:HOH656 4.7 5.8 1.0 CG2 A:VAL168 4.8 6.7 1.0 CA A:ASP318 4.9 5.1 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:15.0 occ:1.00 OD2 B:ASP201 2.1 7.4 1.0 O B:HOH642 2.1 7.6 1.0 O B:HOH714 2.1 10.2 1.0 OD1 B:ASP318 2.2 9.2 1.0 NE2 B:HIS164 2.2 8.1 1.0 NE2 B:HIS200 2.2 7.5 1.0 CG B:ASP318 3.0 12.5 1.0 CD2 B:HIS200 3.1 8.1 1.0 CG B:ASP201 3.1 6.8 1.0 CD2 B:HIS164 3.2 8.3 1.0 CE1 B:HIS164 3.2 8.0 1.0 CE1 B:HIS200 3.2 9.2 1.0 OD2 B:ASP318 3.3 13.9 1.0 OD1 B:ASP201 3.6 6.2 1.0 O B:HOH728 3.7 9.4 1.0 MG B:MG502 3.8 6.9 1.0 O B:HOH737 3.9 20.0 1.0 O B:HOH639 3.9 23.0 1.0 CD2 B:HIS160 4.2 7.7 1.0 CG B:HIS200 4.3 7.5 1.0 ND1 B:HIS164 4.3 9.6 1.0 CB B:ASP201 4.3 6.2 1.0 ND1 B:HIS200 4.3 8.9 1.0 CG B:HIS164 4.3 8.0 1.0 CB B:ASP318 4.5 12.5 1.0 NE2 B:HIS160 4.5 10.5 1.0 O B:HOH636 4.7 8.2 1.0 CG2 B:VAL168 4.8 12.9 1.0 CA B:ASP318 4.9 11.9 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