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Fluorine in PDB 6b97: Crystal Structure of PDE2 in Complex with Complex 9

Enzymatic activity of Crystal Structure of PDE2 in Complex with Complex 9

All present enzymatic activity of Crystal Structure of PDE2 in Complex with Complex 9:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of PDE2 in Complex with Complex 9, PDB code: 6b97 was solved by J.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.06 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.270, 96.070, 102.060, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 22

Other elements in 6b97:

The structure of Crystal Structure of PDE2 in Complex with Complex 9 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Chlorine (Cl) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of PDE2 in Complex with Complex 9 (pdb code 6b97). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Crystal Structure of PDE2 in Complex with Complex 9, PDB code: 6b97:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 6b97

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Fluorine binding site 1 out of 9 in the Crystal Structure of PDE2 in Complex with Complex 9


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Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of PDE2 in Complex with Complex 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:36.8
occ:1.00
 F2 A:CZY1003 0.0 36.8 1.0
C11 A:CZY1003 1.3 33.0 1.0
F A:CZY1003 2.1 37.1 1.0
F1 A:CZY1003 2.1 28.7 1.0
C8 A:CZY1003 2.4 25.9 1.0
C7 A:CZY1003 3.0 24.0 1.0
CB A:THR805 3.2 25.6 1.0
CG2 A:THR805 3.3 23.3 1.0
C9 A:CZY1003 3.5 24.4 1.0
CA A:THR805 3.6 19.6 1.0
CG A:LEU809 3.8 21.7 1.0
O A:THR805 3.9 23.2 1.0
CD1 A:LEU809 3.9 21.6 1.0
C A:THR805 4.2 24.1 1.0
CD2 A:LEU809 4.2 24.1 1.0
CB A:ASP808 4.2 17.4 1.0
C6 A:CZY1003 4.3 22.4 1.0
CD1 A:ILE870 4.3 24.1 1.0
OG1 A:THR805 4.4 27.2 1.0
OD2 A:ASP808 4.5 22.5 1.0
C10 A:CZY1003 4.6 23.6 1.0
O A:THR768 4.7 23.4 1.0
CG A:ASP808 4.8 23.2 1.0
N A:THR805 4.9 19.1 1.0
C5 A:CZY1003 5.0 25.2 1.0

Fluorine binding site 2 out of 9 in 6b97

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Fluorine binding site 2 out of 9 in the Crystal Structure of PDE2 in Complex with Complex 9


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Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of PDE2 in Complex with Complex 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:28.7
occ:1.00
 F1 A:CZY1003 0.0 28.7 1.0
C11 A:CZY1003 1.3 33.0 1.0
F A:CZY1003 2.1 37.1 1.0
F2 A:CZY1003 2.1 36.8 1.0
C8 A:CZY1003 2.4 25.9 1.0
C7 A:CZY1003 3.0 24.0 1.0
O A:THR768 3.2 23.4 1.0
C9 A:CZY1003 3.4 24.4 1.0
CA A:LEU770 3.6 25.3 1.0
N A:LEU770 3.6 23.6 1.0
CG2 A:THR805 3.6 23.3 1.0
C A:THR768 3.7 23.9 1.0
C A:ASP769 3.9 26.2 1.0
O A:ALA767 4.0 24.0 1.0
O A:ASP769 4.1 24.0 1.0
CA A:THR768 4.2 18.7 1.0
CB A:LEU770 4.2 25.4 1.0
CB A:HIS773 4.3 26.7 1.0
C6 A:CZY1003 4.3 22.4 1.0
CB A:THR805 4.3 25.6 1.0
CD1 A:LEU770 4.4 34.1 1.0
N A:ASP769 4.4 20.9 1.0
C10 A:CZY1003 4.6 23.6 1.0
CA A:ASP769 4.7 20.6 1.0
O A:HOH1228 4.8 23.6 1.0
C A:LEU770 4.8 30.7 1.0
CG A:HIS773 4.9 27.8 1.0
CG A:LEU770 5.0 32.0 1.0
C A:ALA767 5.0 23.3 1.0
C5 A:CZY1003 5.0 25.2 1.0

Fluorine binding site 3 out of 9 in 6b97

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Fluorine binding site 3 out of 9 in the Crystal Structure of PDE2 in Complex with Complex 9


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Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of PDE2 in Complex with Complex 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:37.1
occ:1.00
 F A:CZY1003 0.0 37.1 1.0
C11 A:CZY1003 1.3 33.0 1.0
F2 A:CZY1003 2.1 36.8 1.0
F1 A:CZY1003 2.1 28.7 1.0
C8 A:CZY1003 2.4 25.9 1.0
C9 A:CZY1003 2.7 24.4 1.0
CD1 A:LEU770 3.4 34.1 1.0
C7 A:CZY1003 3.6 24.0 1.0
CG2 A:ILE866 3.8 25.6 1.0
CD1 A:ILE870 4.0 24.1 1.0
CD1 A:LEU809 4.1 21.6 1.0
C10 A:CZY1003 4.1 23.6 1.0
CA A:LEU770 4.2 25.3 1.0
CB A:HIS773 4.2 26.7 1.0
CG2 A:THR805 4.3 23.3 1.0
CB A:LEU770 4.3 25.4 1.0
CG A:HIS773 4.3 27.8 1.0
CD2 A:HIS773 4.4 28.1 1.0
CG A:LEU770 4.4 32.0 1.0
CB A:THR805 4.4 25.6 1.0
CG A:LEU809 4.7 21.7 1.0
C6 A:CZY1003 4.8 22.4 1.0
N A:LEU770 4.8 23.6 1.0
CD2 A:LEU809 4.9 24.1 1.0
C5 A:CZY1003 5.0 25.2 1.0

Fluorine binding site 4 out of 9 in 6b97

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Fluorine binding site 4 out of 9 in the Crystal Structure of PDE2 in Complex with Complex 9


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Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of PDE2 in Complex with Complex 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:31.5
occ:0.41
 F2 B:CZY1003 0.0 31.5 0.4
F2 B:CZY1003 0.2 36.5 0.6
C11 B:CZY1003 1.3 31.7 0.4
C11 B:CZY1003 1.3 37.1 0.6
F1 B:CZY1003 2.1 39.1 0.6
F B:CZY1003 2.1 35.7 0.4
F1 B:CZY1003 2.1 32.0 0.4
F B:CZY1003 2.2 37.9 0.6
C8 B:CZY1003 2.3 33.7 0.6
C8 B:CZY1003 2.3 26.0 0.4
C9 B:CZY1003 3.0 34.1 0.6
C9 B:CZY1003 3.2 25.7 0.4
O B:THR768 3.2 23.9 1.0
C7 B:CZY1003 3.3 23.3 0.4
C7 B:CZY1003 3.3 32.1 0.6
CA B:LEU770 3.5 23.1 1.0
N B:LEU770 3.6 22.0 1.0
C B:THR768 3.8 23.1 1.0
CB B:LEU770 3.9 24.1 1.0
C B:ASP769 3.9 23.3 1.0
CG2 B:THR805 4.0 22.1 1.0
O B:ASP769 4.2 24.2 1.0
CD1 B:LEU770 4.2 26.9 1.0
CB B:HIS773 4.3 22.8 1.0
C10 B:CZY1003 4.3 32.4 0.6
O B:ALA767 4.3 22.2 1.0
CA B:THR768 4.3 19.7 1.0
C10 B:CZY1003 4.4 23.0 0.4
C6 B:CZY1003 4.5 21.6 0.4
C6 B:CZY1003 4.5 31.6 0.6
N B:ASP769 4.5 20.4 1.0
O B:HOH1248 4.6 34.2 1.0
CB B:THR805 4.7 23.9 1.0
CG B:LEU770 4.7 26.9 1.0
CA B:ASP769 4.7 20.1 1.0
C B:LEU770 4.8 27.0 1.0
CG B:HIS773 4.8 24.4 1.0
C5 B:CZY1003 4.9 31.3 0.6
C5 B:CZY1003 5.0 20.9 0.4

Fluorine binding site 5 out of 9 in 6b97

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Fluorine binding site 5 out of 9 in the Crystal Structure of PDE2 in Complex with Complex 9


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of PDE2 in Complex with Complex 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:36.5
occ:0.59
 F2 B:CZY1003 0.0 36.5 0.6
F2 B:CZY1003 0.2 31.5 0.4
C11 B:CZY1003 1.3 31.7 0.4
C11 B:CZY1003 1.3 37.1 0.6
F B:CZY1003 2.0 35.7 0.4
F1 B:CZY1003 2.1 32.0 0.4
F1 B:CZY1003 2.1 39.1 0.6
F B:CZY1003 2.1 37.9 0.6
C8 B:CZY1003 2.3 33.7 0.6
C8 B:CZY1003 2.4 26.0 0.4
C9 B:CZY1003 3.0 34.1 0.6
C9 B:CZY1003 3.2 25.7 0.4
O B:THR768 3.3 23.9 1.0
C7 B:CZY1003 3.3 23.3 0.4
C7 B:CZY1003 3.4 32.1 0.6
CA B:LEU770 3.6 23.1 1.0
N B:LEU770 3.7 22.0 1.0
CG2 B:THR805 3.8 22.1 1.0
C B:THR768 3.8 23.1 1.0
C B:ASP769 4.0 23.3 1.0
CB B:LEU770 4.1 24.1 1.0
O B:ASP769 4.2 24.2 1.0
O B:ALA767 4.2 22.2 1.0
CB B:HIS773 4.2 22.8 1.0
CA B:THR768 4.3 19.7 1.0
C10 B:CZY1003 4.3 32.4 0.6
CD1 B:LEU770 4.3 26.9 1.0
C10 B:CZY1003 4.5 23.0 0.4
CB B:THR805 4.5 23.9 1.0
N B:ASP769 4.5 20.4 1.0
C6 B:CZY1003 4.6 21.6 0.4
C6 B:CZY1003 4.6 31.6 0.6
O B:HOH1248 4.8 34.2 1.0
CG B:HIS773 4.8 24.4 1.0
CA B:ASP769 4.8 20.1 1.0
CG B:LEU770 4.9 26.9 1.0
C B:LEU770 4.9 27.0 1.0
C5 B:CZY1003 5.0 31.3 0.6

Fluorine binding site 6 out of 9 in 6b97

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Fluorine binding site 6 out of 9 in the Crystal Structure of PDE2 in Complex with Complex 9


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of PDE2 in Complex with Complex 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:32.0
occ:0.41
 F1 B:CZY1003 0.0 32.0 0.4
F1 B:CZY1003 0.4 39.1 0.6
C11 B:CZY1003 1.2 37.1 0.6
C11 B:CZY1003 1.3 31.7 0.4
F B:CZY1003 1.7 37.9 0.6
F2 B:CZY1003 2.1 36.5 0.6
F2 B:CZY1003 2.1 31.5 0.4
F B:CZY1003 2.1 35.7 0.4
C8 B:CZY1003 2.3 33.7 0.6
C8 B:CZY1003 2.4 26.0 0.4
C7 B:CZY1003 2.8 23.3 0.4
C7 B:CZY1003 2.9 32.1 0.6
C9 B:CZY1003 3.5 34.1 0.6
C9 B:CZY1003 3.6 25.7 0.4
CD1 B:LEU770 3.7 26.9 1.0
CD1 B:ILE870 3.8 24.0 1.0
CG2 B:ILE866 3.9 26.6 1.0
CD1 B:LEU809 4.0 22.0 1.0
C6 B:CZY1003 4.2 21.6 0.4
C6 B:CZY1003 4.2 31.6 0.6
CG2 B:THR805 4.3 22.1 1.0
CD2 B:HIS773 4.3 25.5 1.0
CB B:THR805 4.4 23.9 1.0
CG B:HIS773 4.4 24.4 1.0
CB B:LEU770 4.5 24.1 1.0
CB B:HIS773 4.5 22.8 1.0
CA B:LEU770 4.6 23.1 1.0
CG B:LEU809 4.6 23.2 1.0
CG B:LEU770 4.7 26.9 1.0
C10 B:CZY1003 4.7 32.4 0.6
C10 B:CZY1003 4.8 23.0 0.4
CD2 B:LEU809 4.8 23.2 1.0
NE2 B:HIS773 5.0 24.9 1.0

Fluorine binding site 7 out of 9 in 6b97

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Fluorine binding site 7 out of 9 in the Crystal Structure of PDE2 in Complex with Complex 9


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of PDE2 in Complex with Complex 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:39.1
occ:0.59
 F1 B:CZY1003 0.0 39.1 0.6
F1 B:CZY1003 0.4 32.0 0.4
C11 B:CZY1003 1.3 37.1 0.6
C11 B:CZY1003 1.5 31.7 0.4
F B:CZY1003 2.1 37.9 0.6
F2 B:CZY1003 2.1 31.5 0.4
F2 B:CZY1003 2.1 36.5 0.6
C8 B:CZY1003 2.4 33.7 0.6
C8 B:CZY1003 2.4 26.0 0.4
F B:CZY1003 2.4 35.7 0.4
C7 B:CZY1003 2.7 23.3 0.4
C7 B:CZY1003 2.8 32.1 0.6
CD1 B:LEU770 3.3 26.9 1.0
C9 B:CZY1003 3.6 34.1 0.6
C9 B:CZY1003 3.7 25.7 0.4
CG2 B:ILE866 3.7 26.6 1.0
C6 B:CZY1003 4.1 21.6 0.4
CD1 B:ILE870 4.1 24.0 1.0
CB B:LEU770 4.1 24.1 1.0
C6 B:CZY1003 4.1 31.6 0.6
CA B:LEU770 4.2 23.1 1.0
CD2 B:HIS773 4.2 25.5 1.0
CG B:LEU770 4.3 26.9 1.0
CD1 B:LEU809 4.3 22.0 1.0
CG B:HIS773 4.4 24.4 1.0
CB B:HIS773 4.4 22.8 1.0
CG2 B:THR805 4.5 22.1 1.0
CB B:THR805 4.7 23.9 1.0
C10 B:CZY1003 4.8 32.4 0.6
C10 B:CZY1003 4.8 23.0 0.4
CG B:LEU809 4.9 23.2 1.0
N B:LEU770 4.9 22.0 1.0
C5 B:CZY1003 5.0 20.9 0.4
NE2 B:HIS773 5.0 24.9 1.0
C5 B:CZY1003 5.0 31.3 0.6

Fluorine binding site 8 out of 9 in 6b97

Go back to Fluorine Binding Sites List in 6b97
Fluorine binding site 8 out of 9 in the Crystal Structure of PDE2 in Complex with Complex 9


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of PDE2 in Complex with Complex 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:35.7
occ:0.41
 F B:CZY1003 0.0 35.7 0.4
F B:CZY1003 0.6 37.9 0.6
C11 B:CZY1003 1.3 31.7 0.4
C11 B:CZY1003 1.4 37.1 0.6
F2 B:CZY1003 2.0 36.5 0.6
F2 B:CZY1003 2.1 31.5 0.4
F1 B:CZY1003 2.1 32.0 0.4
C8 B:CZY1003 2.3 33.7 0.6
C8 B:CZY1003 2.3 26.0 0.4
F1 B:CZY1003 2.4 39.1 0.6
C9 B:CZY1003 2.7 34.1 0.6
C9 B:CZY1003 2.8 25.7 0.4
CG2 B:THR805 3.3 22.1 1.0
CB B:THR805 3.3 23.9 1.0
C7 B:CZY1003 3.6 32.1 0.6
C7 B:CZY1003 3.6 23.3 0.4
CA B:THR805 3.7 19.7 1.0
C10 B:CZY1003 4.0 32.4 0.6
O B:THR805 4.0 22.2 1.0
C10 B:CZY1003 4.2 23.0 0.4
CG B:LEU809 4.2 23.2 1.0
CB B:ASP808 4.3 17.7 1.0
CD1 B:LEU809 4.3 22.0 1.0
OD2 B:ASP808 4.3 23.6 1.0
O B:THR768 4.4 23.9 1.0
C B:THR805 4.4 21.2 1.0
CD2 B:LEU809 4.5 23.2 1.0
CD1 B:ILE870 4.5 24.0 1.0
OG1 B:THR805 4.6 24.8 1.0
C6 B:CZY1003 4.7 31.6 0.6
CG B:ASP808 4.7 24.0 1.0
C6 B:CZY1003 4.7 21.6 0.4
CA B:THR768 4.8 19.7 1.0
C5 B:CZY1003 4.9 31.3 0.6
C B:THR768 4.9 23.1 1.0
N B:THR805 4.9 18.2 1.0
C5 B:CZY1003 5.0 20.9 0.4
O B:ALA767 5.0 22.2 1.0

Fluorine binding site 9 out of 9 in 6b97

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Fluorine binding site 9 out of 9 in the Crystal Structure of PDE2 in Complex with Complex 9


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of PDE2 in Complex with Complex 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:37.9
occ:0.59
 F B:CZY1003 0.0 37.9 0.6
F B:CZY1003 0.6 35.7 0.4
C11 B:CZY1003 1.3 31.7 0.4
C11 B:CZY1003 1.3 37.1 0.6
F1 B:CZY1003 1.7 32.0 0.4
F1 B:CZY1003 2.1 39.1 0.6
F2 B:CZY1003 2.1 36.5 0.6
F2 B:CZY1003 2.2 31.5 0.4
C8 B:CZY1003 2.3 33.7 0.6
C8 B:CZY1003 2.4 26.0 0.4
C9 B:CZY1003 2.9 34.1 0.6
C9 B:CZY1003 3.0 25.7 0.4
CB B:THR805 3.3 23.9 1.0
CG2 B:THR805 3.4 22.1 1.0
C7 B:CZY1003 3.5 23.3 0.4
C7 B:CZY1003 3.5 32.1 0.6
CA B:THR805 3.8 19.7 1.0
CD1 B:LEU809 3.9 22.0 1.0
CG B:LEU809 4.0 23.2 1.0
O B:THR805 4.0 22.2 1.0
CD1 B:ILE870 4.0 24.0 1.0
C10 B:CZY1003 4.2 32.4 0.6
C B:THR805 4.3 21.2 1.0
CD2 B:LEU809 4.4 23.2 1.0
C10 B:CZY1003 4.4 23.0 0.4
OG1 B:THR805 4.5 24.8 1.0
CB B:ASP808 4.6 17.7 1.0
C6 B:CZY1003 4.6 31.6 0.6
C6 B:CZY1003 4.7 21.6 0.4
O B:THR768 4.8 23.9 1.0
OD2 B:ASP808 4.8 23.6 1.0
C5 B:CZY1003 5.0 31.3 0.6

Reference:

A.B.Forster, P.Abeywickrema, J.Bunda, C.D.Cox, T.D.Cabalu, M.Egbertson, J.Fay, K.Getty, D.Hall, M.Kornienko, J.Lu, G.Parthasarathy, J.Reid, S.Sharma, W.D.Shipe, S.M.Smith, S.Soisson, S.J.Stachel, H.P.Su, D.Wang, R.Berger. The Identification of A Novel Lead Class For Phosphodiesterase 2 Inhibition By Fragment-Based Drug Design. Bioorg. Med. Chem. Lett. V. 27 5167 2017.
ISSN: ESSN 1464-3405
PubMed: 29113762
DOI: 10.1016/J.BMCL.2017.10.054
Page generated: Thu Aug 1 18:01:01 2024

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