Zinc in PDB 5ohj: Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor.

All present enzymatic activity of Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor.:
3.1.4.53;

The structure of Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor., PDB code: 5ohj was solved by A.Rizzi, L.Carzaniga, E.Armani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.61 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.270, 55.730, 225.560, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.2

The structure of Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor. also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Zinc atom in the Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor. (pdb code 5ohj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor., PDB code: 5ohj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn699 b:13.3 occ:1.00 NE2 A:HIS410 2.1 9.8 1.0 NE2 A:HIS446 2.1 9.7 1.0 OD2 A:ASP447 2.2 10.7 1.0 OD1 A:ASP564 2.2 11.0 1.0 O A:HOH745 2.2 15.6 1.0 O A:HOH714 2.4 16.3 1.0 CD2 A:HIS446 3.0 10.9 1.0 CD2 A:HIS410 3.0 9.4 1.0 CE1 A:HIS446 3.1 10.2 1.0 CE1 A:HIS410 3.1 9.1 1.0 CG A:ASP564 3.1 11.8 1.0 CG A:ASP447 3.2 10.6 1.0 OD2 A:ASP564 3.3 13.0 1.0 OD1 A:ASP447 3.7 10.0 1.0 MG A:MG700 4.0 7.0 1.0 O A:HOH737 4.2 11.9 1.0 CG A:HIS446 4.2 10.5 1.0 ND1 A:HIS446 4.2 10.1 1.0 ND1 A:HIS410 4.2 9.7 1.0 CG A:HIS410 4.2 9.7 1.0 CD2 A:HIS406 4.2 11.3 1.0 CB A:ASP447 4.4 9.9 1.0 O A:HOH748 4.4 14.2 1.0 CB A:ASP564 4.5 11.6 1.0 NE2 A:HIS406 4.5 12.2 1.0 CG2 A:VAL414 4.7 9.9 1.0 O A:HOH747 4.8 11.4 1.0 CA A:ASP564 5.0 10.7 1.0

Zinc binding site 2 out of 2 in the Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn699 b:15.0 occ:1.00 NE2 B:HIS410 2.1 13.7 1.0 OD2 B:ASP447 2.1 13.9 1.0 NE2 B:HIS446 2.1 13.8 1.0 OD1 B:ASP564 2.2 13.6 1.0 O B:HOH752 2.2 17.8 1.0 O B:HOH702 2.4 20.9 1.0 CG B:ASP564 3.1 13.4 1.0 CE1 B:HIS410 3.1 11.9 1.0 CD2 B:HIS410 3.1 13.1 1.0 CD2 B:HIS446 3.1 14.5 1.0 CE1 B:HIS446 3.1 14.1 1.0 CG B:ASP447 3.2 14.8 1.0 OD2 B:ASP564 3.3 14.0 1.0 OD1 B:ASP447 3.7 13.8 1.0 MG B:MG700 4.0 10.4 1.0 O B:HOH725 4.2 14.4 1.0 ND1 B:HIS410 4.2 12.8 1.0 ND1 B:HIS446 4.2 14.5 1.0 CG B:HIS410 4.2 12.9 1.0 CD2 B:HIS406 4.2 13.8 1.0 CG B:HIS446 4.2 14.4 1.0 O B:HOH748 4.3 18.0 1.0 CB B:ASP447 4.4 14.4 1.0 NE2 B:HIS406 4.4 14.3 1.0 CB B:ASP564 4.5 13.4 1.0 CG2 B:VAL414 4.6 11.4 1.0 O B:HOH747 4.9 13.6 1.0 CA B:ASP564 4.9 12.7 1.0

L.Carzaniga, G.Amari, A.Rizzi, C.Capaldi, R.De Fanti, E.Ghidini, G.Villetti, C.Carnini, N.Moretto, F.Facchinetti, P.Caruso, G.Marchini, L.Battipaglia, R.Patacchini, V.Cenacchi, R.Volta, F.Amadei, A.Pappani, S.Capacchi, V.Bagnacani, M.Delcanale, P.Puccini, S.Catinella, M.Civelli, E.Armani. Discovery and Optimization of Thiazolidinyl and Pyrrolidinyl Derivatives As Inhaled PDE4 Inhibitors For Respiratory Diseases. J. Med. Chem. V. 60 10026 2017.
ISSN: ISSN 1520-4804
PubMed: 29200281
DOI: 10.1021/ACS.JMEDCHEM.7B01044