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Fluorine in PDB 6cyc: PDE2 in Complex with Compound 5

Enzymatic activity of PDE2 in Complex with Compound 5

All present enzymatic activity of PDE2 in Complex with Compound 5:
3.1.4.17;

Protein crystallography data

The structure of PDE2 in Complex with Compound 5, PDB code: 6cyc was solved by J.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.17 / 1.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.250, 96.410, 101.650, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 20.5

Other elements in 6cyc:

The structure of PDE2 in Complex with Compound 5 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 PDE2 in Complex with Compound 5 (pdb code 6cyc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the PDE2 in Complex with Compound 5, PDB code: 6cyc:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6cyc

Go back to Fluorine Binding Sites List in 6cyc
Fluorine binding site 1 out of 6 in the PDE2 in Complex with Compound 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of PDE2 in Complex with Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:25.4
occ:1.00
 F2 A:FKJ1003 0.0 25.4 1.0
C10 A:FKJ1003 1.3 23.4 1.0
F1 A:FKJ1003 2.1 20.5 1.0
F A:FKJ1003 2.1 24.5 1.0
C7 A:FKJ1003 2.3 15.3 1.0
C6 A:FKJ1003 2.7 15.5 1.0
CG2 A:THR805 3.3 16.4 1.0
OD2 A:ASP808 3.5 15.5 1.0
C8 A:FKJ1003 3.6 15.3 1.0
CB A:THR805 3.7 19.2 1.0
O A:THR768 3.7 15.2 1.0
CB A:ASP808 3.8 13.1 1.0
CA A:THR805 3.8 13.3 1.0
CG A:ASP808 4.0 14.8 1.0
CA A:THR768 4.0 14.3 1.0
C5 A:FKJ1003 4.1 14.4 1.0
C A:THR768 4.2 15.7 1.0
O A:THR805 4.3 16.2 1.0
CB A:THR768 4.6 17.8 1.0
C A:THR805 4.6 16.7 1.0
O A:ALA767 4.6 17.4 1.0
CG A:LEU809 4.7 16.3 1.0
C9 A:FKJ1003 4.7 15.2 1.0
CD2 A:LEU809 4.9 17.8 1.0
N A:THR805 4.9 13.9 1.0
C4 A:FKJ1003 4.9 16.3 1.0
CD1 A:LEU809 5.0 15.1 1.0

Fluorine binding site 2 out of 6 in 6cyc

Go back to Fluorine Binding Sites List in 6cyc
Fluorine binding site 2 out of 6 in the PDE2 in Complex with Compound 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of PDE2 in Complex with Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:20.5
occ:1.00
 F1 A:FKJ1003 0.0 20.5 1.0
C10 A:FKJ1003 1.3 23.4 1.0
F2 A:FKJ1003 2.1 25.4 1.0
F A:FKJ1003 2.1 24.5 1.0
C7 A:FKJ1003 2.3 15.3 1.0
C8 A:FKJ1003 3.1 15.3 1.0
C6 A:FKJ1003 3.2 15.5 1.0
O A:THR768 3.4 15.2 1.0
CA A:LEU770 3.4 15.1 1.0
N A:LEU770 3.5 16.1 1.0
CB A:LEU770 3.8 15.9 1.0
C A:THR768 3.9 15.7 1.0
C A:ASP769 3.9 17.2 1.0
CG2 A:THR805 3.9 16.4 1.0
O A:ASP769 4.1 16.1 1.0
CD1 A:LEU770 4.1 19.9 1.0
CB A:HIS773 4.3 18.8 1.0
CA A:THR768 4.4 14.3 1.0
O A:ALA767 4.4 17.4 1.0
C9 A:FKJ1003 4.4 15.2 1.0
C5 A:FKJ1003 4.5 14.4 1.0
N A:ASP769 4.5 14.7 1.0
CB A:THR805 4.6 19.2 1.0
CG A:LEU770 4.6 20.3 1.0
C A:LEU770 4.7 19.1 1.0
CA A:ASP769 4.7 14.1 1.0
CG A:HIS773 4.9 21.1 1.0
C4 A:FKJ1003 5.0 16.3 1.0
O1 A:EDO1006 5.0 21.2 1.0

Fluorine binding site 3 out of 6 in 6cyc

Go back to Fluorine Binding Sites List in 6cyc
Fluorine binding site 3 out of 6 in the PDE2 in Complex with Compound 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of PDE2 in Complex with Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:24.5
occ:1.00
 F A:FKJ1003 0.0 24.5 1.0
C10 A:FKJ1003 1.3 23.4 1.0
F1 A:FKJ1003 2.1 20.5 1.0
F2 A:FKJ1003 2.1 25.4 1.0
C7 A:FKJ1003 2.3 15.3 1.0
C8 A:FKJ1003 2.8 15.3 1.0
C6 A:FKJ1003 3.5 15.5 1.0
CD1 A:LEU809 3.6 15.1 1.0
CB A:THR805 3.7 19.2 1.0
CG2 A:THR805 3.7 16.4 1.0
CG A:LEU809 4.0 16.3 1.0
CD1 A:ILE870 4.0 19.9 1.0
C9 A:FKJ1003 4.2 15.2 1.0
CD2 A:LEU809 4.4 17.8 1.0
CA A:THR805 4.4 13.3 1.0
CD1 A:LEU770 4.4 19.9 1.0
CG2 A:ILE866 4.4 19.6 1.0
O A:THR805 4.5 16.2 1.0
C5 A:FKJ1003 4.7 14.4 1.0
OG1 A:THR805 4.8 19.3 1.0
CB A:HIS773 4.8 18.8 1.0
CG A:HIS773 4.9 21.1 1.0
C A:THR805 4.9 16.7 1.0
C4 A:FKJ1003 4.9 16.3 1.0

Fluorine binding site 4 out of 6 in 6cyc

Go back to Fluorine Binding Sites List in 6cyc
Fluorine binding site 4 out of 6 in the PDE2 in Complex with Compound 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of PDE2 in Complex with Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:23.2
occ:1.00
 F2 B:FKJ1003 0.0 23.2 1.0
C10 B:FKJ1003 1.3 22.8 1.0
F1 B:FKJ1003 2.1 21.7 1.0
F B:FKJ1003 2.1 26.4 1.0
C7 B:FKJ1003 2.3 14.6 1.0
C8 B:FKJ1003 3.1 17.1 1.0
CA B:LEU770 3.3 15.3 1.0
C6 B:FKJ1003 3.3 17.3 1.0
O B:THR768 3.4 15.2 1.0
N B:LEU770 3.4 14.8 1.0
CB B:LEU770 3.6 15.8 1.0
C B:ASP769 3.9 17.5 1.0
C B:THR768 3.9 16.2 1.0
CD1 B:LEU770 4.0 19.0 1.0
CG2 B:THR805 4.1 16.8 1.0
O B:ASP769 4.2 17.0 1.0
CB B:HIS773 4.3 16.3 1.0
C9 B:FKJ1003 4.4 14.4 1.0
CG B:LEU770 4.4 19.1 1.0
CA B:THR768 4.5 13.6 1.0
C5 B:FKJ1003 4.5 15.1 1.0
O B:ALA767 4.5 17.4 1.0
C B:LEU770 4.6 17.5 1.0
N B:ASP769 4.6 14.1 1.0
C1 B:EDO1004 4.7 23.1 1.0
CB B:THR805 4.7 15.3 1.0
CA B:ASP769 4.8 14.6 1.0
O1 B:EDO1004 4.8 19.8 1.0
CG B:HIS773 4.8 17.5 1.0
O B:LEU770 5.0 17.7 1.0
C4 B:FKJ1003 5.0 13.4 1.0

Fluorine binding site 5 out of 6 in 6cyc

Go back to Fluorine Binding Sites List in 6cyc
Fluorine binding site 5 out of 6 in the PDE2 in Complex with Compound 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of PDE2 in Complex with Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:21.7
occ:1.00
 F1 B:FKJ1003 0.0 21.7 1.0
C10 B:FKJ1003 1.3 22.8 1.0
F2 B:FKJ1003 2.1 23.2 1.0
F B:FKJ1003 2.1 26.4 1.0
C7 B:FKJ1003 2.3 14.6 1.0
C8 B:FKJ1003 2.8 17.1 1.0
C6 B:FKJ1003 3.5 17.3 1.0
CB B:THR805 3.7 15.3 1.0
CG2 B:THR805 3.7 16.8 1.0
CD1 B:LEU809 3.8 15.4 1.0
CD1 B:ILE870 3.9 17.1 1.0
CG B:LEU809 4.1 16.1 1.0
C9 B:FKJ1003 4.2 14.4 1.0
CD1 B:LEU770 4.4 19.0 1.0
CD2 B:LEU809 4.4 16.3 1.0
CA B:THR805 4.4 13.2 1.0
CG2 B:ILE866 4.5 19.6 1.0
O B:THR805 4.6 16.0 1.0
C5 B:FKJ1003 4.6 15.1 1.0
CG B:HIS773 4.8 17.5 1.0
OG1 B:THR805 4.8 16.6 1.0
CB B:HIS773 4.9 16.3 1.0
CD2 B:HIS773 4.9 19.3 1.0
C4 B:FKJ1003 4.9 13.4 1.0
C B:THR805 5.0 15.8 1.0
CA B:LEU770 5.0 15.3 1.0

Fluorine binding site 6 out of 6 in 6cyc

Go back to Fluorine Binding Sites List in 6cyc
Fluorine binding site 6 out of 6 in the PDE2 in Complex with Compound 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of PDE2 in Complex with Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:26.4
occ:1.00
 F B:FKJ1003 0.0 26.4 1.0
C10 B:FKJ1003 1.3 22.8 1.0
F2 B:FKJ1003 2.1 23.2 1.0
F1 B:FKJ1003 2.1 21.7 1.0
C7 B:FKJ1003 2.4 14.6 1.0
C6 B:FKJ1003 2.7 17.3 1.0
CG2 B:THR805 3.4 16.8 1.0
O B:THR768 3.5 15.2 1.0
OD2 B:ASP808 3.6 16.2 1.0
C8 B:FKJ1003 3.6 17.1 1.0
CB B:THR805 3.7 15.3 1.0
CA B:THR768 3.9 13.6 1.0
CA B:THR805 3.9 13.2 1.0
CB B:ASP808 4.0 12.5 1.0
C B:THR768 4.0 16.2 1.0
C5 B:FKJ1003 4.1 15.1 1.0
CG B:ASP808 4.2 16.9 1.0
CB B:THR768 4.4 15.8 1.0
O B:ALA767 4.5 17.4 1.0
O B:THR805 4.5 16.0 1.0
C9 B:FKJ1003 4.8 14.4 1.0
C B:THR805 4.8 15.8 1.0
CG B:LEU809 4.9 16.1 1.0
CG2 B:THR768 4.9 16.7 1.0
C4 B:FKJ1003 5.0 13.4 1.0
N B:THR805 5.0 12.5 1.0

Reference:

S.J.Stachel, R.Berger, A.B.Nomland, A.T.Ginnetti, D.V.Paone, D.Wang, V.Puri, H.Lange, J.Drott, J.Lu, J.Marcus, M.P.Dwyer, S.Suon, J.M.Uslaner, S.M.Smith. Structure-Guided Design and Procognitive Assessment of A Potent and Selective Phosphodiesterase 2A Inhibitor. Acs Med Chem Lett V. 9 815 2018.
ISSN: ISSN 1948-5875
PubMed: 30128073
DOI: 10.1021/ACSMEDCHEMLETT.8B00214
Page generated: Tue Jul 15 10:31:04 2025

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