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Fluorine in PDB 6b96: Crystal Structure of PDE2 in Complex with Compound 16

Enzymatic activity of Crystal Structure of PDE2 in Complex with Compound 16

All present enzymatic activity of Crystal Structure of PDE2 in Complex with Compound 16:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of PDE2 in Complex with Compound 16, PDB code: 6b96 was solved by J.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.29 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.330, 96.710, 102.350, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 20.7

Other elements in 6b96:

The structure of Crystal Structure of PDE2 in Complex with Compound 16 also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of PDE2 in Complex with Compound 16 (pdb code 6b96). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of PDE2 in Complex with Compound 16, PDB code: 6b96:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6b96

Go back to Fluorine Binding Sites List in 6b96
Fluorine binding site 1 out of 6 in the Crystal Structure of PDE2 in Complex with Compound 16


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 PDE2 in Complex with Compound 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:34.4
occ:1.00
 F2 A:CZV1003 0.0 34.4 1.0
C11 A:CZV1003 1.3 31.0 1.0
F A:CZV1003 2.1 33.2 1.0
F1 A:CZV1003 2.2 27.8 1.0
C8 A:CZV1003 2.4 26.0 1.0
C9 A:CZV1003 2.8 25.6 1.0
CD1 A:LEU809 3.5 21.9 1.0
C7 A:CZV1003 3.6 23.9 1.0
CD1 A:ILE870 3.8 30.1 1.0
CG A:LEU809 3.9 22.6 1.0
CB A:THR805 3.9 28.1 1.0
CG2 A:ILE866 4.0 26.1 1.0
CD1 A:LEU770 4.0 28.8 1.0
CG2 A:THR805 4.1 26.2 1.0
C10 A:CZV1003 4.2 24.4 1.0
CD2 A:LEU809 4.2 27.2 1.0
CA A:THR805 4.7 20.6 1.0
O A:THR805 4.7 23.1 1.0
C6 A:CZV1003 4.7 22.9 1.0
CB A:HIS773 4.8 26.4 1.0
CG A:HIS773 4.9 29.7 1.0
OG1 A:THR805 4.9 28.8 1.0
CA A:LEU770 5.0 24.1 1.0
CB A:LEU770 5.0 24.3 1.0
CD2 A:HIS773 5.0 31.7 1.0
C5 A:CZV1003 5.0 24.4 1.0

Fluorine binding site 2 out of 6 in 6b96

Go back to Fluorine Binding Sites List in 6b96
Fluorine binding site 2 out of 6 in the Crystal Structure of PDE2 in Complex with Compound 16


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 PDE2 in Complex with Compound 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:27.8
occ:1.00
 F1 A:CZV1003 0.0 27.8 1.0
C11 A:CZV1003 1.3 31.0 1.0
F A:CZV1003 2.1 33.2 1.0
F2 A:CZV1003 2.2 34.4 1.0
C8 A:CZV1003 2.4 26.0 1.0
C7 A:CZV1003 3.2 23.9 1.0
C9 A:CZV1003 3.2 25.6 1.0
O A:THR768 3.4 24.1 1.0
CA A:LEU770 3.5 24.1 1.0
N A:LEU770 3.6 23.8 1.0
C A:THR768 3.9 25.4 1.0
CG2 A:THR805 3.9 26.2 1.0
CB A:LEU770 3.9 24.3 1.0
C A:ASP769 4.0 27.2 1.0
CD1 A:LEU770 4.0 28.8 1.0
O A:ASP769 4.2 26.8 1.0
CB A:HIS773 4.4 26.4 1.0
O A:ALA767 4.4 22.9 1.0
C6 A:CZV1003 4.4 22.9 1.0
CA A:THR768 4.4 20.4 1.0
C10 A:CZV1003 4.4 24.4 1.0
CB A:THR805 4.5 28.1 1.0
N A:ASP769 4.6 23.1 1.0
CG A:LEU770 4.6 29.4 1.0
O A:HOH1222 4.6 30.1 1.0
C A:LEU770 4.8 28.8 1.0
CA A:ASP769 4.8 23.1 1.0
C5 A:CZV1003 5.0 24.4 1.0
OD2 A:ASP808 5.0 28.4 1.0

Fluorine binding site 3 out of 6 in 6b96

Go back to Fluorine Binding Sites List in 6b96
Fluorine binding site 3 out of 6 in the Crystal Structure of PDE2 in Complex with Compound 16


Mono view


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 Compound 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:33.2
occ:1.00
 F A:CZV1003 0.0 33.2 1.0
C11 A:CZV1003 1.3 31.0 1.0
F2 A:CZV1003 2.1 34.4 1.0
F1 A:CZV1003 2.1 27.8 1.0
C8 A:CZV1003 2.4 26.0 1.0
C7 A:CZV1003 2.8 23.9 1.0
CG2 A:THR805 3.5 26.2 1.0
CB A:THR805 3.5 28.1 1.0
C9 A:CZV1003 3.6 25.6 1.0
OD2 A:ASP808 3.6 28.4 1.0
CA A:THR805 3.7 20.6 1.0
CB A:ASP808 3.7 19.5 1.0
O A:THR805 4.0 23.1 1.0
CG A:ASP808 4.0 22.8 1.0
O A:THR768 4.1 24.1 1.0
C6 A:CZV1003 4.1 22.9 1.0
CG A:LEU809 4.2 22.6 1.0
C A:THR805 4.4 24.6 1.0
CD2 A:LEU809 4.4 27.2 1.0
CD1 A:LEU809 4.5 21.9 1.0
CA A:THR768 4.6 20.4 1.0
C A:THR768 4.6 25.4 1.0
C10 A:CZV1003 4.7 24.4 1.0
N A:THR805 4.8 19.8 1.0
OG1 A:THR805 4.9 28.8 1.0
C5 A:CZV1003 5.0 24.4 1.0

Fluorine binding site 4 out of 6 in 6b96

Go back to Fluorine Binding Sites List in 6b96
Fluorine binding site 4 out of 6 in the Crystal Structure of PDE2 in Complex with Compound 16


Mono view


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 Compound 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:35.1
occ:1.00
 F2 B:CZV1003 0.0 35.1 1.0
C11 B:CZV1003 1.3 33.6 1.0
F1 B:CZV1003 2.1 38.0 1.0
F B:CZV1003 2.1 34.7 1.0
C8 B:CZV1003 2.3 26.4 1.0
C9 B:CZV1003 3.2 22.7 1.0
C7 B:CZV1003 3.2 24.2 1.0
O B:THR768 3.3 22.7 1.0
CA B:LEU770 3.5 24.1 1.0
N B:LEU770 3.6 24.1 1.0
CB B:LEU770 3.8 23.6 1.0
C B:THR768 4.0 24.4 1.0
CG2 B:THR805 4.0 27.8 1.0
C B:ASP769 4.1 26.9 1.0
CD1 B:LEU770 4.1 26.5 1.0
O B:ASP769 4.4 26.2 1.0
C10 B:CZV1003 4.4 24.6 1.0
C6 B:CZV1003 4.4 23.2 1.0
O2 B:EDO1004 4.5 42.0 1.0
CB B:HIS773 4.5 26.1 1.0
CA B:THR768 4.6 19.9 1.0
CG B:LEU770 4.6 27.6 1.0
C2 B:EDO1004 4.6 44.0 1.0
O B:ALA767 4.7 23.6 1.0
N B:ASP769 4.7 23.0 1.0
CB B:THR805 4.7 26.4 1.0
C B:LEU770 4.8 29.0 1.0
CA B:ASP769 4.8 22.8 1.0
C5 B:CZV1003 4.9 23.7 1.0

Fluorine binding site 5 out of 6 in 6b96

Go back to Fluorine Binding Sites List in 6b96
Fluorine binding site 5 out of 6 in the Crystal Structure of PDE2 in Complex with Compound 16


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 Compound 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:38.0
occ:1.00
 F1 B:CZV1003 0.0 38.0 1.0
C11 B:CZV1003 1.3 33.6 1.0
F2 B:CZV1003 2.1 35.1 1.0
F B:CZV1003 2.1 34.7 1.0
C8 B:CZV1003 2.4 26.4 1.0
C7 B:CZV1003 2.8 24.2 1.0
CG2 B:THR805 3.4 27.8 1.0
CB B:THR805 3.6 26.4 1.0
C9 B:CZV1003 3.6 22.7 1.0
OD2 B:ASP808 3.7 28.0 1.0
CA B:THR805 3.8 19.8 1.0
CB B:ASP808 3.9 18.1 1.0
O B:THR768 4.1 22.7 1.0
O B:THR805 4.1 22.7 1.0
CG B:ASP808 4.1 25.3 1.0
C6 B:CZV1003 4.1 23.2 1.0
CG B:LEU809 4.3 24.0 1.0
C B:THR805 4.5 23.1 1.0
CD2 B:LEU809 4.5 26.0 1.0
CA B:THR768 4.6 19.9 1.0
C B:THR768 4.7 24.4 1.0
CD1 B:LEU809 4.7 24.0 1.0
C10 B:CZV1003 4.7 24.6 1.0
OG1 B:THR805 4.9 26.4 1.0
N B:THR805 4.9 19.8 1.0
C5 B:CZV1003 5.0 23.7 1.0

Fluorine binding site 6 out of 6 in 6b96

Go back to Fluorine Binding Sites List in 6b96
Fluorine binding site 6 out of 6 in the Crystal Structure of PDE2 in Complex with Compound 16


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 Compound 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:34.7
occ:1.00
 F B:CZV1003 0.0 34.7 1.0
C11 B:CZV1003 1.3 33.6 1.0
F2 B:CZV1003 2.1 35.1 1.0
F1 B:CZV1003 2.1 38.0 1.0
C8 B:CZV1003 2.4 26.4 1.0
C9 B:CZV1003 2.8 22.7 1.0
C7 B:CZV1003 3.6 24.2 1.0
CD1 B:ILE870 3.8 29.4 1.0
CD1 B:LEU809 3.8 24.0 1.0
CG2 B:ILE866 4.0 28.6 1.0
CD1 B:LEU770 4.1 26.5 1.0
CB B:THR805 4.1 26.4 1.0
CG2 B:THR805 4.1 27.8 1.0
CG B:LEU809 4.1 24.0 1.0
C10 B:CZV1003 4.2 24.6 1.0
CD2 B:LEU809 4.4 26.0 1.0
C6 B:CZV1003 4.7 23.2 1.0
CD2 B:HIS773 4.7 30.9 1.0
CG B:HIS773 4.8 29.0 1.0
O B:THR805 4.8 22.7 1.0
CA B:THR805 4.9 19.8 1.0
CB B:LEU770 4.9 23.6 1.0
CB B:HIS773 4.9 26.1 1.0
CA B:LEU770 5.0 24.1 1.0

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: Tue Jul 15 09:59:43 2025

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