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Fluorine in PDB 6cyd: PDE2 in Complex with Compound 7

Enzymatic activity of PDE2 in Complex with Compound 7

All present enzymatic activity of PDE2 in Complex with Compound 7:
3.1.4.17;

Protein crystallography data

The structure of PDE2 in Complex with Compound 7, PDB code: 6cyd was solved by J.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.91 / 1.69
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.940, 91.820, 102.830, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21

Other elements in 6cyd:

The structure of PDE2 in Complex with Compound 7 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 7 (pdb code 6cyd). 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 7, PDB code: 6cyd:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6cyd

Go back to Fluorine Binding Sites List in 6cyd
Fluorine binding site 1 out of 6 in the PDE2 in Complex with Compound 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:24.2
occ:1.00
 F2 A:FKG1003 0.0 24.2 1.0
C10 A:FKG1003 1.3 23.8 1.0
F A:FKG1003 2.1 22.7 1.0
F1 A:FKG1003 2.1 29.4 1.0
C7 A:FKG1003 2.3 19.0 1.0
C6 A:FKG1003 3.1 17.7 1.0
O A:THR768 3.2 15.4 1.0
C8 A:FKG1003 3.3 19.7 1.0
CA A:LEU770 3.4 17.1 1.0
N A:LEU770 3.4 17.6 1.0
C A:THR768 3.7 15.8 1.0
C A:ASP769 3.7 16.8 1.0
CB A:LEU770 3.9 17.5 1.0
O A:ASP769 4.0 16.2 1.0
CG2 A:THR805 4.0 16.1 1.0
CD1 A:LEU770 4.2 22.7 1.0
CA A:THR768 4.3 14.0 1.0
O A:ALA767 4.3 17.3 1.0
C5 A:FKG1003 4.4 19.8 1.0
N A:ASP769 4.4 13.0 1.0
CB A:HIS773 4.4 14.4 1.0
C9 A:FKG1003 4.5 19.6 1.0
CA A:ASP769 4.6 14.1 1.0
O1 A:EDO1005 4.6 32.5 1.0
C A:LEU770 4.7 21.9 1.0
CG A:LEU770 4.7 21.9 1.0
CB A:THR805 4.7 17.0 1.0
C1 A:EDO1005 4.8 36.1 1.0
C4 A:FKG1003 5.0 18.6 1.0

Fluorine binding site 2 out of 6 in 6cyd

Go back to Fluorine Binding Sites List in 6cyd
Fluorine binding site 2 out of 6 in the PDE2 in Complex with Compound 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:29.4
occ:1.00
 F1 A:FKG1003 0.0 29.4 1.0
C10 A:FKG1003 1.3 23.8 1.0
F A:FKG1003 2.1 22.7 1.0
F2 A:FKG1003 2.1 24.2 1.0
C7 A:FKG1003 2.4 19.0 1.0
C8 A:FKG1003 2.8 19.7 1.0
CG2 A:THR805 3.4 16.1 1.0
OD2 A:ASP808 3.5 16.7 1.0
O A:THR768 3.6 15.4 1.0
C6 A:FKG1003 3.6 17.7 1.0
CB A:ASP808 3.7 15.0 1.0
CB A:THR805 3.8 17.0 1.0
CA A:THR805 3.9 14.7 1.0
CA A:THR768 4.0 14.0 1.0
CG A:ASP808 4.0 16.3 1.0
C A:THR768 4.1 15.8 1.0
C9 A:FKG1003 4.1 19.6 1.0
O A:THR805 4.4 15.4 1.0
CB A:THR768 4.5 18.5 1.0
O A:ALA767 4.5 17.3 1.0
CG A:LEU809 4.7 18.6 1.0
C A:THR805 4.7 16.4 1.0
C5 A:FKG1003 4.7 19.8 1.0
CD2 A:LEU809 4.8 17.8 1.0
C4 A:FKG1003 5.0 18.6 1.0
N A:THR805 5.0 13.6 1.0

Fluorine binding site 3 out of 6 in 6cyd

Go back to Fluorine Binding Sites List in 6cyd
Fluorine binding site 3 out of 6 in the PDE2 in Complex with Compound 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:22.7
occ:1.00
 F A:FKG1003 0.0 22.7 1.0
C10 A:FKG1003 1.3 23.8 1.0
F2 A:FKG1003 2.1 24.2 1.0
F1 A:FKG1003 2.1 29.4 1.0
C7 A:FKG1003 2.3 19.0 1.0
C6 A:FKG1003 2.8 17.7 1.0
C8 A:FKG1003 3.5 19.7 1.0
CD1 A:LEU809 3.7 18.0 1.0
CG2 A:THR805 3.7 16.1 1.0
CB A:THR805 3.8 17.0 1.0
CG A:LEU809 4.0 18.6 1.0
C5 A:FKG1003 4.1 19.8 1.0
CD1 A:ILE870 4.2 19.6 1.0
CD2 A:LEU809 4.3 17.8 1.0
CG2 A:ILE866 4.3 18.1 1.0
CD1 A:LEU770 4.4 22.7 1.0
CA A:THR805 4.5 14.7 1.0
C9 A:FKG1003 4.6 19.6 1.0
O A:THR805 4.7 15.4 1.0
CB A:HIS773 4.8 14.4 1.0
OG1 A:THR805 4.9 17.9 1.0
C4 A:FKG1003 4.9 18.6 1.0
CA A:LEU770 5.0 17.1 1.0
CG A:HIS773 5.0 17.2 1.0

Fluorine binding site 4 out of 6 in 6cyd

Go back to Fluorine Binding Sites List in 6cyd
Fluorine binding site 4 out of 6 in the PDE2 in Complex with Compound 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:24.8
occ:1.00
 F2 B:FKG1003 0.0 24.8 1.0
C10 B:FKG1003 1.3 27.2 1.0
F B:FKG1003 2.1 28.3 1.0
F1 B:FKG1003 2.1 31.4 1.0
C7 B:FKG1003 2.4 19.7 1.0
C6 B:FKG1003 3.1 20.0 1.0
C8 B:FKG1003 3.3 22.5 1.0
O B:THR768 3.4 17.5 1.0
CA B:LEU770 3.4 20.4 1.0
N B:LEU770 3.5 19.3 1.0
CB B:LEU770 3.7 21.2 1.0
C B:THR768 4.0 19.5 1.0
CD1 B:LEU770 4.0 24.5 1.0
C B:ASP769 4.0 19.5 1.0
C1 B:EDO1004 4.0 29.3 1.0
CG2 B:THR805 4.1 17.7 1.0
O B:ASP769 4.3 18.6 1.0
C5 B:FKG1003 4.4 20.7 1.0
CG B:LEU770 4.5 25.1 1.0
O1 B:EDO1004 4.5 27.3 1.0
CB B:HIS773 4.5 17.6 1.0
CA B:THR768 4.6 15.7 1.0
C9 B:FKG1003 4.6 18.2 1.0
N B:ASP769 4.7 14.9 1.0
O B:ALA767 4.7 18.5 1.0
C B:LEU770 4.8 23.1 1.0
CB B:THR805 4.8 19.0 1.0
CA B:ASP769 4.8 14.7 1.0

Fluorine binding site 5 out of 6 in 6cyd

Go back to Fluorine Binding Sites List in 6cyd
Fluorine binding site 5 out of 6 in the PDE2 in Complex with Compound 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:31.4
occ:1.00
 F1 B:FKG1003 0.0 31.4 1.0
C10 B:FKG1003 1.3 27.2 1.0
F B:FKG1003 2.1 28.3 1.0
F2 B:FKG1003 2.1 24.8 1.0
C7 B:FKG1003 2.4 19.7 1.0
C8 B:FKG1003 2.8 22.5 1.0
CG2 B:THR805 3.5 17.7 1.0
OD2 B:ASP808 3.6 18.5 1.0
C6 B:FKG1003 3.6 20.0 1.0
CB B:THR805 3.7 19.0 1.0
CB B:ASP808 3.8 13.1 1.0
CA B:THR805 3.8 15.1 1.0
O B:THR768 4.0 17.5 1.0
CG B:ASP808 4.0 18.9 1.0
C9 B:FKG1003 4.2 18.2 1.0
O B:THR805 4.2 16.7 1.0
CG B:LEU809 4.4 18.4 1.0
CA B:THR768 4.5 15.7 1.0
C B:THR768 4.5 19.5 1.0
CD2 B:LEU809 4.6 20.1 1.0
C B:THR805 4.6 18.4 1.0
C5 B:FKG1003 4.8 20.7 1.0
CD1 B:LEU809 4.8 20.0 1.0
CB B:THR768 4.9 16.6 1.0
N B:THR805 5.0 15.3 1.0
O B:ALA767 5.0 18.5 1.0

Fluorine binding site 6 out of 6 in 6cyd

Go back to Fluorine Binding Sites List in 6cyd
Fluorine binding site 6 out of 6 in the PDE2 in Complex with Compound 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:28.3
occ:1.00
 F B:FKG1003 0.0 28.3 1.0
C10 B:FKG1003 1.3 27.2 1.0
F1 B:FKG1003 2.1 31.4 1.0
F2 B:FKG1003 2.1 24.8 1.0
C7 B:FKG1003 2.3 19.7 1.0
C6 B:FKG1003 2.8 20.0 1.0
C8 B:FKG1003 3.5 22.5 1.0
CD1 B:LEU809 3.7 20.0 1.0
CG B:LEU809 4.0 18.4 1.0
CD1 B:ILE870 4.0 19.6 1.0
CB B:THR805 4.0 19.0 1.0
CG2 B:THR805 4.0 17.7 1.0
CD1 B:LEU770 4.1 24.5 1.0
C5 B:FKG1003 4.1 20.7 1.0
CG2 B:ILE866 4.2 20.4 1.0
CD2 B:LEU809 4.2 20.1 1.0
C9 B:FKG1003 4.6 18.2 1.0
CA B:THR805 4.7 15.1 1.0
O B:THR805 4.8 16.7 1.0
CB B:LEU770 4.9 21.2 1.0
C4 B:FKG1003 4.9 19.4 1.0
CA B:LEU770 5.0 20.4 1.0
CB B:HIS773 5.0 17.6 1.0
CG B:HIS773 5.0 21.1 1.0
CD2 B:HIS773 5.0 22.9 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: Thu Aug 1 18:42:41 2024

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