Fluorine in PDB 6a3n: Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2

Enzymatic activity of Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2

All present enzymatic activity of Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2:
3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2, PDB code: 6a3n was solved by Y.N.Wu, Q.Zhou, Y.P.Chen, H.B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.46 / 2.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 104.110, 104.110, 269.079, 90.00, 90.00, 90.00
R / Rfree (%) 24.8 / 28

Other elements in 6a3n:

The structure of Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2 also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2 (pdb code 6a3n). 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 the PDE9 Catalytic Domain in Complex with Inhibitor 2, PDB code: 6a3n:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 6a3n

Go back to Fluorine Binding Sites List in 6a3n
Fluorine binding site 1 out of 2 in the Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2


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 the PDE9 Catalytic Domain in Complex with Inhibitor 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:32.8
occ:1.00
F26 A:9Q9603 0.0 32.8 1.0
C24 A:9Q9603 1.4 33.3 1.0
C25 A:9Q9603 2.4 33.3 1.0
C23 A:9Q9603 2.4 33.8 1.0
N21 A:9Q9603 3.4 33.3 1.0
C22 A:9Q9603 3.5 33.8 1.0
C16 A:9Q9603 3.6 31.5 1.0
C17 A:9Q9603 4.1 31.5 1.0
C13 A:9Q9603 4.1 30.9 1.0
CB A:MET365 4.1 21.0 1.0
CG A:MET365 4.2 20.9 1.0
OH A:TYR424 4.2 29.3 1.0
CE1 A:PHE456 4.3 21.7 1.0
CE A:MET365 4.5 20.4 1.0
C1 A:9Q9603 4.6 32.3 1.0
O A:HOH736 4.7 18.9 1.0
N5 A:9Q9603 4.7 29.6 1.0
C18 A:9Q9603 4.8 31.0 1.0
CD1 A:PHE456 4.9 21.7 1.0
N10 A:9Q9603 5.0 30.4 1.0

Fluorine binding site 2 out of 2 in 6a3n

Go back to Fluorine Binding Sites List in 6a3n
Fluorine binding site 2 out of 2 in the Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2


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 the PDE9 Catalytic Domain in Complex with Inhibitor 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F603

b:30.4
occ:1.00
F26 B:9Q9603 0.0 30.4 1.0
C24 B:9Q9603 1.4 31.0 1.0
C23 B:9Q9603 2.4 31.3 1.0
C25 B:9Q9603 2.4 30.0 1.0
C22 B:9Q9603 2.9 30.9 1.0
N21 B:9Q9603 3.1 30.3 1.0
C16 B:9Q9603 3.2 23.1 1.0
CG B:MET365 3.9 24.9 1.0
CE1 B:PHE456 4.0 22.2 1.0
C13 B:9Q9603 4.0 23.1 1.0
CB B:MET365 4.1 24.5 1.0
CE B:MET365 4.1 24.5 1.0
C1 B:9Q9603 4.3 29.7 1.0
C17 B:9Q9603 4.5 23.5 1.0
N5 B:9Q9603 4.6 23.9 1.0
CD1 B:PHE456 4.6 22.4 1.0
OH B:TYR424 4.6 27.7 1.0
SD B:MET365 4.8 25.0 1.0
N10 B:9Q9603 4.8 23.2 1.0
CZ B:PHE456 4.9 22.3 1.0
O B:HOH787 4.9 13.8 1.0
O B:HOH792 4.9 19.4 1.0

Reference:

Y.Wu, Q.Zhou, T.Zhang, Z.Li, Y.P.Chen, P.Zhang, Y.F.Yu, H.Geng, Y.J.Tian, C.Zhang, Y.Wang, J.W.Chen, Y.Chen, H.B.Luo. Discovery of Potent, Selective, and Orally Bioavailable Inhibitors Against Phosphodiesterase-9, A Novel Target For the Treatment of Vascular Dementia. J. Med. Chem. V. 62 4218 2019.
ISSN: ISSN 1520-4804
PubMed: 30916555
DOI: 10.1021/ACS.JMEDCHEM.8B01041
Page generated: Sun Dec 13 12:44:06 2020

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