Chlorine in PDB 6b98: PDE2 in Complex with Compound 1

All present enzymatic activity of PDE2 in Complex with Compound 1:
3.1.4.17;

The structure of PDE2 in Complex with Compound 1, PDB code: 6b98 was solved by J.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.09 / 1.97
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.034, 94.186, 102.526, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 24

The structure of PDE2 in Complex with Compound 1 also contains other interesting chemical elements:

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

The binding sites of Chlorine atom in the PDE2 in Complex with Compound 1 (pdb code 6b98). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the PDE2 in Complex with Compound 1, PDB code: 6b98:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the PDE2 in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of PDE2 in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1003 b:57.4 occ:1.00 CL A:D071003 0.0 57.4 1.0 C4 A:D071003 1.7 52.6 1.0 N2 A:D071003 2.6 49.5 1.0 N3 A:D071003 2.7 51.8 1.0 O A:HOH1178 3.0 21.7 1.0 NE2 A:GLN812 3.3 25.3 1.0 O A:HOH1152 3.7 46.4 1.0 OE1 A:GLN859 3.7 42.4 1.0 CG2 A:ILE822 3.7 26.4 1.0 O A:HOH1176 3.7 27.6 1.0 C1 A:D071003 3.8 50.3 1.0 C5 A:D071003 3.9 52.9 1.0 CE2 A:PHE862 4.1 37.8 1.0 CG2 A:ILE826 4.1 31.4 1.0 CD A:GLN812 4.2 38.2 1.0 CD2 A:PHE862 4.3 35.0 1.0 C A:D071003 4.4 51.2 1.0 NE2 A:GLN859 4.5 28.9 1.0 CD A:GLN859 4.5 47.9 1.0 OE1 A:GLN812 4.8 34.2 1.0 CZ A:PHE862 4.8 36.0 1.0 CD1 A:ILE826 4.9 41.4 1.0 CB A:ILE826 4.9 29.6 1.0 N4 A:D071003 4.9 56.9 1.0 C A:ILE822 4.9 26.2 1.0 O A:ILE822 5.0 25.1 1.0 N A:ALA823 5.0 23.0 1.0 N A:D071003 5.0 50.9 1.0 CA A:ALA823 5.0 22.9 1.0

Chlorine binding site 2 out of 2 in the PDE2 in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of PDE2 in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1003 b:57.4 occ:1.00 CL B:D071003 0.0 57.4 1.0 C4 B:D071003 1.7 53.5 1.0 N2 B:D071003 2.6 50.5 1.0 N3 B:D071003 2.6 52.1 1.0 O B:HOH1127 2.9 24.4 1.0 NE2 B:GLN859 3.3 52.7 1.0 NE2 B:GLN812 3.5 32.3 1.0 CD1 B:ILE826 3.6 49.3 1.0 OE1 B:GLN859 3.7 59.8 1.0 C1 B:D071003 3.8 49.0 1.0 C5 B:D071003 3.9 51.0 1.0 CD B:GLN859 3.9 62.7 1.0 CG2 B:ILE822 4.0 27.6 1.0 O B:HOH1170 4.0 32.2 1.0 CE2 B:PHE862 4.3 39.7 1.0 C B:D071003 4.4 49.4 1.0 CG2 B:ILE826 4.5 36.2 1.0 CD2 B:PHE862 4.5 37.1 1.0 CD B:GLN812 4.5 41.9 1.0 CG1 B:ILE826 4.5 36.2 1.0 CB B:ILE826 4.6 33.3 1.0 CA B:ALA823 4.6 27.2 1.0 N B:ALA823 4.7 27.5 1.0 C B:ILE822 4.8 30.4 1.0 O B:ILE822 4.9 27.7 1.0 N4 B:D071003 4.9 54.0 1.0 N B:D071003 5.0 48.7 1.0 CB B:ALA823 5.0 27.5 1.0

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