Fluorine in PDB 7vtv: Crystal Structure of PDE8A Catalytic Domain in Complex with 15

All present enzymatic activity of Crystal Structure of PDE8A Catalytic Domain in Complex with 15:
3.1.4.53;

The structure of Crystal Structure of PDE8A Catalytic Domain in Complex with 15, PDB code: 7vtv was solved by X.-N.Wu, Q.Zhou, Y.-D.Huang, Z.Li, Y.Wu, H.-B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.17 / 2.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	75.986, 131.724, 101.456, 90, 90, 90
R / Rfree (%)	28.2 / 32.4

The structure of Crystal Structure of PDE8A Catalytic Domain in Complex with 15 also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Zinc	(Zn)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Fluorine atom in the Crystal Structure of PDE8A Catalytic Domain in Complex with 15 (pdb code 7vtv). 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 PDE8A Catalytic Domain in Complex with 15, PDB code: 7vtv:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of PDE8A Catalytic Domain in Complex with 15


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 PDE8A Catalytic Domain in Complex with 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:F903 b:33.3 occ:1.00 FAU A:7ZZ903 0.0 33.3 1.0 CAT A:7ZZ903 1.4 32.7 1.0 FAV A:7ZZ903 2.3 33.0 1.0 CAS A:7ZZ903 2.4 32.2 1.0 O A:THR668 2.6 26.4 1.0 O A:HOH1037 2.7 28.3 1.0 O A:GLU669 3.1 27.9 1.0 C A:GLU669 3.4 28.3 1.0 C A:THR668 3.4 26.2 1.0 CA A:MET670 3.6 29.5 1.0 OAR A:7ZZ903 3.6 31.1 1.0 N A:MET670 3.7 28.9 1.0 N A:GLU669 4.2 27.1 1.0 CA A:THR668 4.2 25.6 1.0 NZ A:LYS723 4.3 17.8 1.0 CA A:GLU669 4.3 27.8 1.0 CB A:MET670 4.5 30.0 1.0 CAP A:7ZZ903 4.6 30.0 1.0 C A:MET670 4.6 29.4 1.0 O A:MET670 4.7 29.7 1.0 ND1 A:HIS673 4.8 26.8 1.0 CG A:MET670 4.8 30.4 1.0 O A:ALA667 4.8 23.9 1.0 OD2 A:ASP726 4.9 17.4 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of PDE8A Catalytic Domain in Complex with 15


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 PDE8A Catalytic Domain in Complex with 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:F903 b:33.0 occ:1.00 FAV A:7ZZ903 0.0 33.0 1.0 CAT A:7ZZ903 1.4 32.7 1.0 FAU A:7ZZ903 2.3 33.3 1.0 CAS A:7ZZ903 2.4 32.2 1.0 OAR A:7ZZ903 2.6 31.1 1.0 ND1 A:HIS673 3.2 26.8 1.0 CB A:HIS673 3.5 26.4 1.0 CA A:MET670 3.5 29.5 1.0 O A:MET670 3.7 29.7 1.0 CG A:HIS673 3.7 26.6 1.0 CAP A:7ZZ903 3.8 30.0 1.0 CG A:MET670 3.9 30.4 1.0 O A:GLU669 4.1 27.9 1.0 C A:MET670 4.1 29.4 1.0 CD2 A:PHE785 4.2 27.0 1.0 CAO A:7ZZ903 4.2 29.9 1.0 CB A:MET670 4.2 30.0 1.0 NZ A:LYS723 4.2 17.8 1.0 CE2 A:PHE785 4.2 27.2 1.0 CE1 A:HIS673 4.3 26.9 1.0 CA A:HIS673 4.3 26.4 1.0 N A:MET670 4.4 28.9 1.0 O A:HOH1037 4.4 28.3 1.0 C A:GLU669 4.5 28.3 1.0 N A:HIS673 4.8 27.0 1.0 SD A:MET670 4.8 31.1 1.0 O A:THR668 4.8 26.4 1.0 CAQ A:7ZZ903 4.9 29.4 1.0 CD2 A:HIS673 5.0 26.8 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of PDE8A Catalytic Domain in Complex with 15


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 PDE8A Catalytic Domain in Complex with 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:F903 b:29.7 occ:1.00 FAZ A:7ZZ903 0.0 29.7 1.0 CAY A:7ZZ903 1.3 29.5 1.0 FBA A:7ZZ903 2.1 29.3 1.0 OAW A:7ZZ903 2.2 29.8 1.0 CAN A:7ZZ903 2.7 29.5 1.0 CD1 A:PHE781 3.1 23.4 1.0 CAM A:7ZZ903 3.3 29.3 1.0 CE1 A:PHE785 3.4 26.9 1.0 CE1 A:PHE781 3.4 23.2 1.0 CAO A:7ZZ903 3.5 29.9 1.0 CL2 A:7ZZ903 3.5 27.3 1.0 N3 A:7ZZ903 3.9 27.6 1.0 CZ A:PHE785 3.9 27.1 1.0 C2 A:7ZZ903 4.0 27.4 1.0 CD1 A:PHE785 4.0 26.7 1.0 CG A:PHE781 4.3 23.4 1.0 CAL A:7ZZ903 4.3 29.0 1.0 CAP A:7ZZ903 4.5 30.0 1.0 CZ A:PHE781 4.7 23.2 1.0 CZ A:PHE767 4.8 35.9 1.0 CB A:PHE781 4.8 23.5 1.0 CAQ A:7ZZ903 4.8 29.4 1.0 C4 A:7ZZ903 4.9 27.8 1.0 CE2 A:PHE785 4.9 27.2 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of PDE8A Catalytic Domain in Complex with 15


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 PDE8A Catalytic Domain in Complex with 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:F903 b:29.3 occ:1.00 FBA A:7ZZ903 0.0 29.3 1.0 CAY A:7ZZ903 1.3 29.5 1.0 FAZ A:7ZZ903 2.1 29.7 1.0 OAW A:7ZZ903 2.3 29.8 1.0 CAN A:7ZZ903 3.1 29.5 1.0 CAM A:7ZZ903 3.2 29.3 1.0 CL2 A:7ZZ903 3.4 27.3 1.0 CE1 A:PHE767 3.6 35.9 1.0 CE2 A:TYR748 3.7 30.9 1.0 OH A:TYR748 3.8 31.3 1.0 CZ A:PHE767 3.9 35.9 1.0 N3 A:7ZZ903 3.9 27.6 1.0 CZ A:TYR748 3.9 31.1 1.0 C2 A:7ZZ903 4.2 27.4 1.0 CAO A:7ZZ903 4.3 29.9 1.0 CAL A:7ZZ903 4.5 29.0 1.0 CD2 A:TYR748 4.5 30.9 1.0 CD1 A:PHE767 4.7 35.9 1.0 CE1 A:TYR748 4.9 31.2 1.0 CD1 A:PHE781 4.9 23.4 1.0

X.-N.Wu, Q.Zhou, Y.-D.Huang, Z.Li, Y.Wu, H.-B.Luo. Structure-Based Discovery of Orally Efficient PDE8 Inhibitors For the Treatment of Vascular Dementia To Be Published.