Chlorine in PDB 6b97: 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;

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

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

Fluorine	(F)	9 atoms
Magnesium	(Mg)	2 atoms
Zinc	(Zn)	2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of PDE2 in Complex with Complex 9, PDB code: 6b97:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of PDE2 in Complex with Complex 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl1003 b:56.0 occ:1.00 CL A:CZY1003 0.0 56.0 1.0 C A:CZY1003 1.7 43.1 1.0 N1 A:CZY1003 2.6 35.6 1.0 N A:CZY1003 2.6 38.2 1.0 O A:HOH1227 3.5 53.3 1.0 O A:HOH1110 3.5 45.1 1.0 OH A:TYR827 3.6 31.9 1.0 CD1 A:PHE862 3.6 31.0 1.0 C1 A:CZY1003 3.8 35.2 1.0 C3 A:CZY1003 3.8 34.3 1.0 O A:HOH1119 3.9 26.6 1.0 CE2 A:PHE830 3.9 26.4 1.0 CG A:PHE862 3.9 27.0 1.0 CB A:PHE862 4.0 25.2 1.0 O A:HOH1253 4.1 38.9 1.0 CE1 A:PHE862 4.3 31.6 1.0 SD A:MET847 4.4 36.5 1.0 CZ A:TYR827 4.4 29.7 1.0 C2 A:CZY1003 4.4 32.4 1.0 CZ A:PHE830 4.5 25.6 1.0 CD2 A:PHE862 4.8 29.9 1.0 CE A:MET847 4.9 34.3 1.0 N2 A:CZY1003 4.9 29.4 1.0 CD2 A:PHE830 4.9 22.9 1.0 N4 A:CZY1003 5.0 34.5 1.0 O A:LEU858 5.0 25.5 1.0 CE2 A:TYR827 5.0 25.2 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of PDE2 in Complex with Complex 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 B:Cl1003 b:30.9 occ:0.41 CL B:CZY1003 0.0 30.9 0.4 C B:CZY1003 1.7 26.7 0.4 N3 B:CZY1003 2.0 39.4 0.6 C13 B:CZY1003 2.4 38.7 0.6 N1 B:CZY1003 2.6 25.2 0.4 N B:CZY1003 2.6 25.1 0.4 N4 B:CZY1003 3.3 40.8 0.6 OH B:TYR827 3.7 35.2 1.0 O B:HOH1201 3.7 40.0 1.0 C2 B:CZY1003 3.8 38.0 0.6 C1 B:CZY1003 3.8 25.7 0.4 CD1 B:PHE862 3.8 35.0 1.0 C3 B:CZY1003 3.8 23.6 0.4 CE2 B:PHE830 3.9 29.4 1.0 C14 B:CZY1003 4.0 41.0 0.6 CB B:PHE862 4.0 29.0 1.0 CG B:PHE862 4.1 30.7 1.0 C1 B:CZY1003 4.2 40.0 0.6 SD B:MET847 4.2 44.6 1.0 C2 B:CZY1003 4.4 24.4 0.4 CZ B:TYR827 4.5 32.5 1.0 CZ B:PHE830 4.6 26.7 1.0 CE1 B:PHE862 4.6 36.5 1.0 CE B:MET847 4.7 40.9 1.0 O B:HOH1164 4.8 53.5 1.0 N2 B:CZY1003 4.9 21.4 0.4 O B:LEU858 4.9 26.0 1.0 CD2 B:PHE830 4.9 27.1 1.0 N4 B:CZY1003 5.0 27.9 0.4 CE2 B:TYR827 5.0 26.7 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 B:Cl1003 b:44.0 occ:0.59 CL B:CZY1003 0.0 44.0 0.6 C B:CZY1003 1.7 41.6 0.6 N3 B:CZY1003 1.9 27.0 0.4 N1 B:CZY1003 2.6 42.3 0.6 N B:CZY1003 2.6 38.6 0.6 C13 B:CZY1003 2.7 26.0 0.4 N4 B:CZY1003 3.1 27.9 0.4 OH B:TYR655 3.3 22.9 1.0 O B:HOH1167 3.3 23.9 1.0 NE2 B:GLN812 3.6 25.2 1.0 O B:HOH1211 3.6 25.2 1.0 C14 B:CZY1003 3.6 27.4 0.4 C1 B:CZY1003 3.8 40.0 0.6 CD2 B:LEU809 3.8 23.2 1.0 C3 B:CZY1003 3.9 35.9 0.6 C2 B:CZY1003 4.0 24.4 0.4 CA B:LEU809 4.1 19.8 1.0 CZ B:TYR655 4.1 24.5 1.0 C1 B:CZY1003 4.2 25.7 0.4 CD1 B:ILE826 4.2 37.0 1.0 CG2 B:ILE822 4.3 23.3 1.0 CG B:GLN812 4.3 21.8 1.0 O B:ASP808 4.4 19.8 1.0 CD B:GLN812 4.4 33.1 1.0 C2 B:CZY1003 4.4 38.0 0.6 O B:LEU809 4.5 21.8 1.0 CB B:LEU809 4.6 20.1 1.0 C B:LEU809 4.6 22.0 1.0 CE2 B:PHE862 4.6 36.9 1.0 OD2 B:ASP811 4.6 27.0 1.0 CB B:ASP811 4.6 20.8 1.0 CE1 B:TYR655 4.7 20.8 1.0 CZ B:PHE862 4.7 34.9 1.0 CG B:LEU809 4.8 23.2 1.0 CE2 B:TYR655 4.9 21.0 1.0 N2 B:CZY1003 5.0 33.4 0.6

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