Fluorine 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:

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	2 atoms

The binding sites of Fluorine 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 Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of PDE4D Complexed with A Novel Inhibitor, PDB code: 6imt:
Jump to Fluorine binding site number: 1; 2;

Fluorine 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 Fluorine with other atoms in the F 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:F508 b:0.4 occ:1.00 F1 A:AK0508 0.0 0.4 1.0 C20 A:AK0508 1.4 0.9 1.0 C19 A:AK0508 2.4 0.2 1.0 C21 A:AK0508 2.4 0.9 1.0 C17 A:AK0508 3.6 95.6 1.0 C22 A:AK0508 3.6 93.7 1.0 CA A:PHE372 4.0 12.8 1.0 N A:PHE372 4.0 13.3 1.0 C18 A:AK0508 4.1 85.0 1.0 C A:GLY371 4.3 14.2 1.0 O A:GLY371 4.3 15.3 1.0 CB A:PHE372 4.5 11.9 1.0 SD A:MET357 4.7 22.2 1.0 CE A:MET357 4.7 26.7 1.0 CG1 A:ILE376 4.8 17.2 1.0 CD1 A:PHE372 4.8 13.3 1.0 N2 A:AK0508 4.9 88.6 1.0 O A:SER368 4.9 15.1 1.0

Fluorine 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 Fluorine with other atoms in the F 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:F508 b:0.1 occ:1.00 F1 B:AK0508 0.0 0.1 1.0 C20 B:AK0508 1.4 0.2 1.0 C19 B:AK0508 2.4 0.7 1.0 C21 B:AK0508 2.4 0.9 1.0 C17 B:AK0508 3.6 98.3 1.0 C22 B:AK0508 3.6 98.3 1.0 C18 B:AK0508 4.1 87.2 1.0 CA B:PHE372 4.2 19.6 1.0 N B:PHE372 4.3 19.3 1.0 O B:GLY371 4.5 20.4 1.0 C B:GLY371 4.5 20.1 1.0 CG1 B:ILE376 4.7 24.3 1.0 CB B:PHE372 4.7 20.7 1.0 CD1 B:PHE372 4.8 18.4 1.0 N2 B:AK0508 4.9 89.3 1.0 CE B:MET357 4.9 24.9 1.0 SD B:MET357 5.0 26.0 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