Fluorine 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:

Magnesium	(Mg)	4 atoms
Zinc	(Zn)	4 atoms

The binding sites of Fluorine 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 Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Human PDE1B with Inhibitor 3, PDB code: 5b25:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine 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 Fluorine with other atoms in the F 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:F603 b:28.8 occ:1.00 F38 A:4QJ603 0.0 28.8 1.0 C19 A:4QJ603 1.3 26.0 1.0 N30 A:4QJ603 2.3 23.4 1.0 C12 A:4QJ603 2.4 22.9 1.0 C17 A:4QJ603 3.5 21.7 1.0 C4 A:4QJ603 3.6 21.2 1.0 CZ A:PHE340 3.9 20.5 1.0 C11 A:4QJ603 4.0 21.4 1.0 CE2 A:PHE340 4.2 17.9 1.0 CD1 A:ILE428 4.2 20.7 1.0 C13 A:4QJ603 4.6 19.9 1.0 C6 A:4QJ603 4.8 21.2 1.0

Fluorine 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 Fluorine with other atoms in the F 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:F603 b:28.9 occ:1.00 F38 B:4QJ603 0.0 28.9 1.0 C19 B:4QJ603 1.3 24.4 1.0 N30 B:4QJ603 2.2 23.1 1.0 C12 B:4QJ603 2.4 21.3 1.0 C17 B:4QJ603 3.5 21.0 1.0 C4 B:4QJ603 3.6 21.7 1.0 CZ B:PHE340 3.8 18.2 1.0 C11 B:4QJ603 4.0 21.8 1.0 CD1 B:ILE428 4.1 19.4 1.0 CE2 B:PHE340 4.2 18.6 1.0 C13 B:4QJ603 4.6 19.8 1.0 C6 B:4QJ603 4.8 20.3 1.0 CG1 B:ILE428 4.8 20.1 1.0 CE1 B:PHE340 5.0 18.1 1.0

Fluorine 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 Fluorine with other atoms in the F 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:F603 b:31.7 occ:1.00 F38 C:4QJ603 0.0 31.7 1.0 C19 C:4QJ603 1.3 28.0 1.0 N30 C:4QJ603 2.3 25.3 1.0 C12 C:4QJ603 2.4 26.6 1.0 CG D:GLU441 3.1 31.9 1.0 CB D:PRO474 3.3 26.7 1.0 N D:ASN475 3.5 25.2 1.0 C17 C:4QJ603 3.5 23.4 1.0 OE2 D:GLU441 3.6 44.1 1.0 C4 C:4QJ603 3.6 25.5 1.0 O D:ASN475 3.7 24.7 1.0 C D:PRO474 3.8 24.7 1.0 CA D:PRO474 3.8 26.5 1.0 CD D:GLU441 3.8 36.7 1.0 CZ C:PHE340 3.9 19.9 1.0 C D:ASN475 4.0 24.6 1.0 C11 C:4QJ603 4.0 23.1 1.0 O D:GLU441 4.1 28.1 1.0 CG2 D:VAL478 4.2 22.3 1.0 CD1 C:ILE428 4.2 21.4 1.0 CB D:GLU441 4.3 26.3 1.0 CA D:ASN475 4.3 23.9 1.0 CE2 C:PHE340 4.3 19.0 1.0 CA D:GLU441 4.6 26.0 1.0 O D:PRO474 4.6 24.4 1.0 CG D:PRO474 4.6 29.0 1.0 C13 C:4QJ603 4.6 21.5 1.0 C D:GLU441 4.7 27.4 1.0 N D:PRO476 4.8 25.0 1.0 C6 C:4QJ603 4.8 23.2 1.0

Fluorine 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 Fluorine with other atoms in the F 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:F603 b:32.1 occ:1.00 F38 D:4QJ603 0.0 32.1 1.0 C19 D:4QJ603 1.4 26.7 1.0 N30 D:4QJ603 2.3 24.7 1.0 C12 D:4QJ603 2.4 23.3 1.0 C17 D:4QJ603 3.5 23.4 1.0 C4 D:4QJ603 3.6 22.6 1.0 CZ D:PHE340 3.9 19.6 1.0 C11 D:4QJ603 4.0 22.5 1.0 CD1 D:ILE428 4.1 19.7 1.0 CE2 D:PHE340 4.2 18.0 1.0 C13 D:4QJ603 4.7 21.7 1.0 C6 D:4QJ603 4.8 22.4 1.0 CG1 D:ILE428 5.0 17.9 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