Fluorine in PDB 6cyb: 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: 6cyb was solved by J.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.17 / 1.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.260, 96.640, 102.040, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 20.1

Other elements in 6cyb:

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:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the PDE2 in Complex with Compound 7 (pdb code 6cyb). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the PDE2 in Complex with Compound 7, PDB code: 6cyb:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 6cyb

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Fluorine binding site 1 out of 12 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:F1008

b:21.3
occ:1.00
F5 A:FKV1008 0.0 21.3 1.0
C13 A:FKV1008 1.3 19.3 1.0
F4 A:FKV1008 2.1 18.3 1.0
F3 A:FKV1008 2.1 16.9 1.0
C12 A:FKV1008 2.3 17.3 1.0
C2 A:FKV1008 2.8 17.3 1.0
NE2 A:GLN812 3.2 28.8 1.0
CG A:GLN812 3.2 19.5 1.0
CE2 A:PHE862 3.4 22.1 1.0
C1 A:FKV1008 3.4 16.0 1.0
CZ A:PHE862 3.6 20.1 1.0
O1 A:FKV1008 3.6 17.4 1.0
N A:FKV1008 3.7 14.1 1.0
CD A:GLN812 3.7 34.3 1.0
C14 A:FKV1008 3.8 16.5 1.0
CD2 A:LEU809 3.8 20.0 1.0
O A:LEU809 4.2 16.8 1.0
CA A:LEU809 4.2 13.8 1.0
CB A:LEU809 4.4 14.0 1.0
C A:FKV1008 4.5 15.6 1.0
CD2 A:PHE862 4.5 19.2 1.0
N1 A:FKV1008 4.6 15.4 1.0
CB A:GLN812 4.6 17.6 1.0
C A:LEU809 4.6 16.5 1.0
CG A:LEU809 4.7 18.1 1.0
CE1 A:PHE862 4.8 22.4 1.0
O A:HOH1197 4.9 15.9 1.0
O2 A:EDO1007 4.9 18.5 1.0
OE1 A:GLN812 4.9 29.9 1.0
OH A:TYR655 4.9 17.6 1.0
N A:GLN812 5.0 17.8 1.0

Fluorine binding site 2 out of 12 in 6cyb

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Fluorine binding site 2 out of 12 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:F1008

b:18.3
occ:1.00
F4 A:FKV1008 0.0 18.3 1.0
C13 A:FKV1008 1.3 19.3 1.0
F5 A:FKV1008 2.1 21.3 1.0
F3 A:FKV1008 2.2 16.9 1.0
C12 A:FKV1008 2.3 17.3 1.0
CB A:ASP811 3.4 16.4 1.0
O2 A:EDO1007 3.4 18.5 1.0
NE2 A:GLN812 3.5 28.8 1.0
CG2 A:ILE822 3.6 22.7 1.0
CG A:GLN812 3.6 19.5 1.0
OH A:TYR655 3.6 17.6 1.0
C2 A:FKV1008 3.7 17.3 1.0
OD2 A:ASP811 3.9 21.6 1.0
O A:LEU809 4.0 16.8 1.0
CD A:GLN812 4.0 34.3 1.0
N A:GLN812 4.1 17.8 1.0
CG A:ASP811 4.1 22.1 1.0
CA A:ASP811 4.2 15.5 1.0
N A:ASP811 4.2 14.8 1.0
C A:LEU809 4.4 16.5 1.0
C A:ASP811 4.4 20.6 1.0
CA A:LEU809 4.4 13.8 1.0
CZ A:TYR655 4.5 15.8 1.0
N A:FKV1008 4.5 14.1 1.0
O1 A:FKV1008 4.6 17.4 1.0
C1 A:FKV1008 4.6 16.0 1.0
CE1 A:TYR655 4.6 14.4 1.0
CB A:GLN812 4.7 17.6 1.0
O A:ASP808 4.8 15.8 1.0
C2 A:EDO1007 4.8 24.8 1.0
O A:HOH1197 4.9 15.9 1.0
CB A:ILE822 4.9 20.1 1.0
CA A:GLN812 4.9 16.9 1.0

Fluorine binding site 3 out of 12 in 6cyb

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Fluorine binding site 3 out of 12 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:F1008

b:16.9
occ:1.00
F3 A:FKV1008 0.0 16.9 1.0
C13 A:FKV1008 1.3 19.3 1.0
F5 A:FKV1008 2.1 21.3 1.0
F4 A:FKV1008 2.2 18.3 1.0
C12 A:FKV1008 2.3 17.3 1.0
C2 A:FKV1008 3.0 17.3 1.0
O A:HOH1197 3.0 15.9 1.0
O A:ASP808 3.1 15.8 1.0
N A:FKV1008 3.2 14.1 1.0
CA A:LEU809 3.2 13.8 1.0
OH A:TYR655 3.3 17.6 1.0
O2 A:EDO1007 3.3 18.5 1.0
CD2 A:LEU809 3.3 20.0 1.0
C A:LEU809 3.9 16.5 1.0
C A:ASP808 4.0 17.0 1.0
O A:LEU809 4.0 16.8 1.0
CB A:LEU809 4.0 14.0 1.0
N A:LEU809 4.0 14.5 1.0
C1 A:FKV1008 4.2 16.0 1.0
CZ A:TYR655 4.3 15.8 1.0
CG A:LEU809 4.3 18.1 1.0
N1 A:FKV1008 4.4 15.4 1.0
C2 A:EDO1007 4.5 24.8 1.0
CG A:GLN812 4.7 19.5 1.0
N A:SER810 4.8 14.2 1.0
CZ A:PHE862 4.9 20.1 1.0
C A:FKV1008 4.9 15.6 1.0
CB A:ASP811 4.9 16.4 1.0
OD2 A:ASP811 4.9 21.6 1.0
CE2 A:TYR655 5.0 14.1 1.0

Fluorine binding site 4 out of 12 in 6cyb

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Fluorine binding site 4 out of 12 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
A:F1008

b:21.8
occ:1.00
F2 A:FKV1008 0.0 21.8 1.0
C10 A:FKV1008 1.3 24.4 1.0
F1 A:FKV1008 2.1 28.8 1.0
F A:FKV1008 2.1 26.1 1.0
C7 A:FKV1008 2.3 15.1 1.0
C8 A:FKV1008 3.1 15.5 1.0
C6 A:FKV1008 3.3 16.8 1.0
O A:THR768 3.3 15.4 1.0
CA A:LEU770 3.4 16.1 1.0
N A:LEU770 3.5 16.8 1.0
CB A:LEU770 3.8 16.6 1.0
C A:THR768 3.9 17.2 1.0
C A:ASP769 3.9 18.7 1.0
CG2 A:THR805 4.0 17.6 1.0
CD1 A:LEU770 4.0 21.8 1.0
O A:ASP769 4.2 18.4 1.0
CB A:HIS773 4.4 19.5 1.0
C9 A:FKV1008 4.4 15.8 1.0
CA A:THR768 4.4 15.2 1.0
O A:ALA767 4.5 18.9 1.0
C5 A:FKV1008 4.5 16.8 1.0
CG A:LEU770 4.5 22.1 1.0
N A:ASP769 4.6 15.6 1.0
CB A:THR805 4.7 20.1 1.0
C A:LEU770 4.7 20.3 1.0
CA A:ASP769 4.8 15.4 1.0
C4 A:FKV1008 5.0 17.3 1.0
O A:LEU770 5.0 19.1 1.0

Fluorine binding site 5 out of 12 in 6cyb

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Fluorine binding site 5 out of 12 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
A:F1008

b:28.8
occ:1.00
F1 A:FKV1008 0.0 28.8 1.0
C10 A:FKV1008 1.3 24.4 1.0
F2 A:FKV1008 2.1 21.8 1.0
F A:FKV1008 2.2 26.1 1.0
C7 A:FKV1008 2.3 15.1 1.0
C6 A:FKV1008 2.7 16.8 1.0
OD2 A:ASP808 3.4 17.3 1.0
CG2 A:THR805 3.5 17.6 1.0
C8 A:FKV1008 3.6 15.5 1.0
O A:THR768 3.6 15.4 1.0
CB A:ASP808 3.7 12.1 1.0
CB A:THR805 3.8 20.1 1.0
CA A:THR805 3.9 15.6 1.0
CG A:ASP808 4.0 16.4 1.0
CA A:THR768 4.1 15.2 1.0
C5 A:FKV1008 4.1 16.8 1.0
C A:THR768 4.1 17.2 1.0
O A:THR805 4.4 17.3 1.0
CB A:THR768 4.6 19.3 1.0
CD2 A:LEU809 4.6 20.0 1.0
CG A:LEU809 4.7 18.1 1.0
O A:ALA767 4.7 18.9 1.0
C9 A:FKV1008 4.7 15.8 1.0
C A:THR805 4.7 19.1 1.0
C4 A:FKV1008 4.9 17.3 1.0

Fluorine binding site 6 out of 12 in 6cyb

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Fluorine binding site 6 out of 12 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
A:F1008

b:26.1
occ:1.00
F A:FKV1008 0.0 26.1 1.0
C10 A:FKV1008 1.3 24.4 1.0
F2 A:FKV1008 2.1 21.8 1.0
F1 A:FKV1008 2.2 28.8 1.0
C7 A:FKV1008 2.4 15.1 1.0
C8 A:FKV1008 2.8 15.5 1.0
C6 A:FKV1008 3.6 16.8 1.0
CD1 A:LEU809 3.7 19.1 1.0
CB A:THR805 3.8 20.1 1.0
CG A:LEU809 3.8 18.1 1.0
CG2 A:THR805 3.9 17.6 1.0
CD2 A:LEU809 4.0 20.0 1.0
CD1 A:ILE870 4.0 19.5 1.0
C9 A:FKV1008 4.2 15.8 1.0
CD1 A:LEU770 4.3 21.8 1.0
CG2 A:ILE866 4.4 19.7 1.0
CA A:THR805 4.5 15.6 1.0
O A:THR805 4.6 17.3 1.0
C5 A:FKV1008 4.7 16.8 1.0
OG1 A:THR805 4.9 20.1 1.0
C4 A:FKV1008 5.0 17.3 1.0
C A:THR805 5.0 19.1 1.0
CB A:HIS773 5.0 19.5 1.0

Fluorine binding site 7 out of 12 in 6cyb

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Fluorine binding site 7 out of 12 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 7 of PDE2 in Complex with Compound 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1006

b:19.5
occ:1.00
F5 B:FKV1006 0.0 19.5 1.0
C13 B:FKV1006 1.3 18.0 1.0
F4 B:FKV1006 2.1 18.8 1.0
F3 B:FKV1006 2.2 17.0 1.0
C12 B:FKV1006 2.3 14.2 1.0
C2 B:FKV1006 2.8 15.0 1.0
NE2 B:GLN812 3.1 30.6 1.0
CE2 B:PHE862 3.3 22.5 1.0
CG B:GLN812 3.3 18.6 1.0
C1 B:FKV1006 3.3 15.1 1.0
CZ B:PHE862 3.5 19.8 1.0
O1 B:FKV1006 3.6 19.1 1.0
CD B:GLN812 3.7 29.8 1.0
N B:FKV1006 3.7 15.4 1.0
C14 B:FKV1006 3.7 18.1 1.0
CD2 B:LEU809 4.0 16.9 1.0
O B:LEU809 4.2 15.6 1.0
CA B:LEU809 4.3 14.3 1.0
C B:FKV1006 4.4 16.4 1.0
CB B:LEU809 4.4 14.9 1.0
CD2 B:PHE862 4.4 20.0 1.0
N1 B:FKV1006 4.5 16.0 1.0
C B:LEU809 4.7 15.7 1.0
CB B:GLN812 4.7 15.9 1.0
CE1 B:PHE862 4.7 21.3 1.0
CG B:LEU809 4.7 18.0 1.0
O B:HOH1210 4.9 15.5 1.0
OH B:TYR655 4.9 16.1 1.0
OE1 B:GLN812 4.9 27.1 1.0
CG2 B:ILE822 4.9 22.2 1.0
N2 B:FKV1006 5.0 16.6 1.0
O B:HOH1237 5.0 18.8 1.0

Fluorine binding site 8 out of 12 in 6cyb

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Fluorine binding site 8 out of 12 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 8 of PDE2 in Complex with Compound 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1006

b:18.8
occ:1.00
F4 B:FKV1006 0.0 18.8 1.0
C13 B:FKV1006 1.3 18.0 1.0
F3 B:FKV1006 2.1 17.0 1.0
F5 B:FKV1006 2.1 19.5 1.0
C12 B:FKV1006 2.3 14.2 1.0
CB B:ASP811 3.4 15.6 1.0
NE2 B:GLN812 3.4 30.6 1.0
O B:HOH1237 3.5 18.8 1.0
CG2 B:ILE822 3.5 22.2 1.0
OH B:TYR655 3.5 16.1 1.0
C2 B:FKV1006 3.7 15.0 1.0
CG B:GLN812 3.7 18.6 1.0
OD2 B:ASP811 3.8 19.9 1.0
CD B:GLN812 4.0 29.8 1.0
O B:LEU809 4.1 15.6 1.0
CG B:ASP811 4.1 21.5 1.0
N B:GLN812 4.2 15.4 1.0
N B:ASP811 4.3 14.1 1.0
CA B:ASP811 4.3 14.5 1.0
CZ B:TYR655 4.3 17.5 1.0
C B:LEU809 4.4 15.7 1.0
N B:FKV1006 4.5 15.4 1.0
CA B:LEU809 4.5 14.3 1.0
C B:ASP811 4.5 18.5 1.0
CE1 B:TYR655 4.5 13.8 1.0
C1 B:FKV1006 4.6 15.1 1.0
O1 B:FKV1006 4.6 19.1 1.0
CB B:ILE822 4.8 21.5 1.0
O B:ASP808 4.8 14.5 1.0
O B:HOH1210 4.8 15.5 1.0
CB B:GLN812 4.9 15.9 1.0

Fluorine binding site 9 out of 12 in 6cyb

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Fluorine binding site 9 out of 12 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 9 of PDE2 in Complex with Compound 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1006

b:17.0
occ:1.00
F3 B:FKV1006 0.0 17.0 1.0
C13 B:FKV1006 1.3 18.0 1.0
F4 B:FKV1006 2.1 18.8 1.0
F5 B:FKV1006 2.2 19.5 1.0
C12 B:FKV1006 2.3 14.2 1.0
C2 B:FKV1006 3.0 15.0 1.0
O B:HOH1210 3.0 15.5 1.0
OH B:TYR655 3.1 16.1 1.0
O B:ASP808 3.2 14.5 1.0
N B:FKV1006 3.2 15.4 1.0
CA B:LEU809 3.3 14.3 1.0
O B:HOH1237 3.3 18.8 1.0
CD2 B:LEU809 3.3 16.9 1.0
C B:LEU809 3.9 15.7 1.0
CB B:LEU809 4.0 14.9 1.0
C B:ASP808 4.0 15.8 1.0
O B:LEU809 4.0 15.6 1.0
N B:LEU809 4.1 13.1 1.0
C1 B:FKV1006 4.2 15.1 1.0
CZ B:TYR655 4.2 17.5 1.0
CG B:LEU809 4.3 18.0 1.0
N1 B:FKV1006 4.4 16.0 1.0
CG B:GLN812 4.8 18.6 1.0
OD2 B:ASP811 4.8 19.9 1.0
CZ B:PHE862 4.8 19.8 1.0
N B:SER810 4.8 12.9 1.0
CE2 B:TYR655 4.8 13.2 1.0
C B:FKV1006 4.9 16.4 1.0
CB B:ASP811 4.9 15.6 1.0
NE2 B:GLN812 4.9 30.6 1.0
CE1 B:TYR655 4.9 13.8 1.0
N B:ASP811 5.0 14.1 1.0

Fluorine binding site 10 out of 12 in 6cyb

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Fluorine binding site 10 out of 12 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 10 of PDE2 in Complex with Compound 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1006

b:24.1
occ:1.00
F2 B:FKV1006 0.0 24.1 1.0
C10 B:FKV1006 1.3 24.0 1.0
F B:FKV1006 2.1 27.2 1.0
F1 B:FKV1006 2.1 25.4 1.0
C7 B:FKV1006 2.3 17.4 1.0
C8 B:FKV1006 3.1 18.1 1.0
CA B:LEU770 3.3 17.1 1.0
C6 B:FKV1006 3.3 17.8 1.0
O B:THR768 3.4 17.1 1.0
N B:LEU770 3.5 16.6 1.0
CB B:LEU770 3.7 17.4 1.0
CD1 B:LEU770 3.9 20.5 1.0
C B:ASP769 4.0 18.9 1.0
C B:THR768 4.0 16.9 1.0
CG2 B:THR805 4.1 17.9 1.0
O B:ASP769 4.2 18.8 1.0
CB B:HIS773 4.4 16.9 1.0
C9 B:FKV1006 4.4 17.8 1.0
CG B:LEU770 4.4 21.1 1.0
C5 B:FKV1006 4.5 16.8 1.0
CA B:THR768 4.6 13.7 1.0
O B:ALA767 4.6 17.8 1.0
C B:LEU770 4.7 19.4 1.0
N B:ASP769 4.7 15.0 1.0
C1 B:EDO1005 4.7 24.8 1.0
O1 B:EDO1005 4.8 22.4 1.0
CA B:ASP769 4.8 15.2 1.0
CB B:THR805 4.8 16.7 1.0
CG B:HIS773 4.9 18.8 1.0
C4 B:FKV1006 5.0 17.5 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: Sun Dec 13 12:47:10 2020

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