Zinc in PDB 5b25: Crystal Structure of Human PDE1B with Inhibitor 3

All present enzymatic activity of Crystal Structure of Human PDE1B with Inhibitor 3:
3.1.4.17;

The structure of Crystal Structure of Human PDE1B with Inhibitor 3, PDB code: 5b25 was solved by K.Ida, W.Lane, G.Snell, S.Sogabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	102.875, 102.875, 294.848, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 20.3

The structure of Crystal Structure of Human PDE1B with Inhibitor 3 also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Magnesium	(Mg)	4 atoms

The binding sites of Zinc atom in the Crystal Structure of Human PDE1B with Inhibitor 3 (pdb code 5b25). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human PDE1B with Inhibitor 3, PDB code: 5b25:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Human PDE1B with Inhibitor 3


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 Human PDE1B with Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:31.2 occ:1.00 OD2 A:ASP264 2.0 19.9 1.0 OD1 A:ASP370 2.1 17.9 1.0 NE2 A:HIS227 2.2 18.6 1.0 NE2 A:HIS263 2.3 17.1 1.0 O A:HOH739 2.3 18.1 1.0 O A:HOH733 2.3 15.8 1.0 CG A:ASP370 3.1 19.9 1.0 CD2 A:HIS263 3.1 14.7 1.0 CG A:ASP264 3.1 19.3 1.0 CE1 A:HIS227 3.2 17.5 1.0 CD2 A:HIS227 3.2 18.8 1.0 OD2 A:ASP370 3.3 23.3 1.0 CE1 A:HIS263 3.4 19.0 1.0 OD1 A:ASP264 3.7 17.9 1.0 MG A:MG602 4.0 26.1 1.0 O A:HOH865 4.1 17.8 1.0 CD2 A:HIS223 4.1 15.8 1.0 O A:HOH734 4.2 15.4 1.0 NE2 A:HIS223 4.2 16.8 1.0 CB A:ASP264 4.3 16.3 1.0 CG A:HIS263 4.3 17.3 1.0 ND1 A:HIS227 4.3 18.3 1.0 CG A:HIS227 4.4 17.9 1.0 ND1 A:HIS263 4.4 17.4 1.0 CB A:ASP370 4.4 16.4 1.0 O A:HOH713 4.8 16.6 1.0 CG2 A:VAL231 4.8 15.0 1.0 CA A:ASP370 4.9 16.5 1.0 O A:ASP370 4.9 18.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Human PDE1B with Inhibitor 3


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 Human PDE1B with Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:29.3 occ:1.00 OD2 B:ASP264 2.0 15.9 1.0 OD1 B:ASP370 2.2 18.3 1.0 NE2 B:HIS227 2.2 15.1 1.0 O B:HOH760 2.2 16.5 1.0 O B:HOH702 2.3 15.7 1.0 NE2 B:HIS263 2.3 14.8 1.0 CG B:ASP370 3.1 19.4 1.0 CD2 B:HIS263 3.1 13.6 1.0 CG B:ASP264 3.1 18.2 1.0 CD2 B:HIS227 3.1 15.9 1.0 CE1 B:HIS227 3.2 16.0 1.0 OD2 B:ASP370 3.3 23.2 1.0 CE1 B:HIS263 3.4 13.6 1.0 OD1 B:ASP264 3.7 18.3 1.0 MG B:MG602 4.0 26.9 1.0 O B:HOH862 4.1 17.8 1.0 O B:HOH723 4.1 14.6 1.0 CD2 B:HIS223 4.2 15.2 1.0 CB B:ASP264 4.3 15.0 1.0 CG B:HIS263 4.3 15.2 1.0 CG B:HIS227 4.3 15.6 1.0 ND1 B:HIS227 4.3 17.1 1.0 NE2 B:HIS223 4.4 15.6 1.0 ND1 B:HIS263 4.4 13.2 1.0 CB B:ASP370 4.4 15.5 1.0 O B:HOH714 4.7 17.8 1.0 CG2 B:VAL231 4.8 14.6 1.0 O B:ASP370 4.9 18.3 1.0 CA B:ASP370 4.9 15.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Human PDE1B with Inhibitor 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human PDE1B with Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:29.8 occ:1.00 OD2 C:ASP264 2.1 16.4 1.0 OD1 C:ASP370 2.1 17.4 1.0 NE2 C:HIS227 2.2 16.2 1.0 O C:HOH701 2.3 13.8 1.0 NE2 C:HIS263 2.3 15.9 1.0 O C:HOH765 2.3 18.1 1.0 CG C:ASP370 3.0 19.0 1.0 CD2 C:HIS263 3.1 14.1 1.0 CD2 C:HIS227 3.1 16.4 1.0 CG C:ASP264 3.2 16.0 1.0 CE1 C:HIS227 3.3 17.3 1.0 OD2 C:ASP370 3.3 20.3 1.0 CE1 C:HIS263 3.4 14.9 1.0 OD1 C:ASP264 3.7 14.6 1.0 MG C:MG602 3.9 26.5 1.0 O C:HOH875 4.1 17.6 1.0 CD2 C:HIS223 4.2 13.0 1.0 O C:HOH729 4.2 14.3 1.0 CG C:HIS263 4.3 15.4 1.0 CB C:ASP264 4.3 14.5 1.0 CG C:HIS227 4.3 16.6 1.0 NE2 C:HIS223 4.3 15.7 1.0 ND1 C:HIS227 4.3 15.5 1.0 ND1 C:HIS263 4.4 15.1 1.0 CB C:ASP370 4.4 14.8 1.0 CG2 C:VAL231 4.7 12.9 1.0 O C:HOH708 4.8 18.8 1.0 O C:ASP370 4.8 16.0 1.0 CA C:ASP370 4.9 14.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Human PDE1B with Inhibitor 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human PDE1B with Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:29.7 occ:1.00 OD2 D:ASP264 2.1 18.1 1.0 OD1 D:ASP370 2.1 15.9 1.0 NE2 D:HIS227 2.3 15.9 1.0 O D:HOH703 2.3 14.3 1.0 O D:HOH793 2.3 15.9 1.0 NE2 D:HIS263 2.3 14.7 1.0 CG D:ASP370 3.0 15.5 1.0 CD2 D:HIS263 3.1 15.2 1.0 CG D:ASP264 3.1 18.2 1.0 CD2 D:HIS227 3.2 17.5 1.0 CE1 D:HIS227 3.3 16.1 1.0 OD2 D:ASP370 3.3 19.7 1.0 CE1 D:HIS263 3.4 15.7 1.0 OD1 D:ASP264 3.7 17.5 1.0 MG D:MG602 3.9 28.7 1.0 O D:HOH863 4.0 17.6 1.0 O D:HOH714 4.2 14.7 1.0 CD2 D:HIS223 4.2 16.0 1.0 CB D:ASP264 4.2 16.2 1.0 CG D:HIS263 4.3 16.8 1.0 NE2 D:HIS223 4.3 17.7 1.0 CG D:HIS227 4.3 16.6 1.0 ND1 D:HIS227 4.4 16.8 1.0 CB D:ASP370 4.4 14.5 1.0 ND1 D:HIS263 4.4 16.0 1.0 O D:HOH732 4.8 16.6 1.0 CG2 D:VAL231 4.8 14.7 1.0 O D:ASP370 4.9 16.6 1.0 CA D:ASP370 4.9 13.8 1.0

P.Li, H.Zheng, J.Zhao, L.Zhang, W.Yao, H.Zhu, J.D.Beard, K.Ida, W.Lane, G.Snell, S.Sogabe, C.J.Heyser, G.L.Snyder, J.P.Hendrick, K.E.Vanover, R.E.Davis, L.P.Wennogle. Discovery of Potent and Selective Inhibitors of Phosphodiesterase 1 For the Treatment of Cognitive Impairment Associated with Neurodegenerative and Neuropsychiatric Diseases J.Med.Chem. V. 59 1149 2016.
ISSN: ISSN 0022-2623
PubMed: 26789933
DOI: 10.1021/ACS.JMEDCHEM.5B01751