Zinc in PDB 4jib: Crystal Structure of of PDE2-Inhibitor Complex

All present enzymatic activity of Crystal Structure of of PDE2-Inhibitor Complex:
3.1.4.17;

The structure of Crystal Structure of of PDE2-Inhibitor Complex, PDB code: 4jib was solved by J.Pandit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.72
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	55.880, 74.132, 91.802, 109.67, 88.72, 88.97
R / Rfree (%)	18.8 / 24

The structure of Crystal Structure of of PDE2-Inhibitor Complex also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of of PDE2-Inhibitor Complex (pdb code 4jib). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of of PDE2-Inhibitor Complex, PDB code: 4jib:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of of PDE2-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of of PDE2-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:16.0 occ:1.00 NE2 A:HIS660 2.1 11.8 1.0 NE2 A:HIS696 2.1 8.9 1.0 OD2 A:ASP697 2.1 9.0 1.0 OD1 A:ASP808 2.1 14.0 1.0 O A:HOH1120 2.4 12.2 1.0 O A:HOH1454 2.4 13.1 1.0 CD2 A:HIS696 3.0 10.0 1.0 CE1 A:HIS660 3.1 10.8 1.0 CD2 A:HIS660 3.1 11.9 1.0 CG A:ASP808 3.1 15.9 1.0 CG A:ASP697 3.1 12.1 1.0 CE1 A:HIS696 3.2 9.3 1.0 OD2 A:ASP808 3.4 20.2 1.0 OD1 A:ASP697 3.6 9.9 1.0 MG A:MG1002 3.9 12.2 1.0 CG A:HIS696 4.2 9.8 1.0 ND1 A:HIS660 4.2 9.2 1.0 CG A:HIS660 4.2 10.3 1.0 ND1 A:HIS696 4.2 10.9 1.0 CD2 A:HIS656 4.3 12.7 1.0 O A:HOH1445 4.3 11.1 1.0 O A:HOH1102 4.4 14.1 1.0 CB A:ASP697 4.4 10.2 1.0 NE2 A:HIS656 4.5 17.0 1.0 CB A:ASP808 4.5 11.8 1.0 O A:HOH1269 4.8 9.0 1.0 CG2 A:VAL664 4.8 10.8 1.0 CA A:ASP808 4.9 12.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of of PDE2-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of of PDE2-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:16.7 occ:1.00 NE2 B:HIS660 2.1 13.3 1.0 OD2 B:ASP697 2.1 11.4 1.0 NE2 B:HIS696 2.1 10.3 1.0 OD1 B:ASP808 2.2 13.2 1.0 O B:HOH1456 2.3 13.1 1.0 O B:HOH1103 2.4 14.5 1.0 CD2 B:HIS660 3.0 13.0 1.0 CD2 B:HIS696 3.0 11.2 1.0 CG B:ASP808 3.1 16.1 1.0 CG B:ASP697 3.1 11.2 1.0 CE1 B:HIS660 3.2 11.9 1.0 CE1 B:HIS696 3.2 11.1 1.0 OD2 B:ASP808 3.3 19.3 1.0 OD1 B:ASP697 3.6 9.0 1.0 MG B:MG1002 3.9 12.6 1.0 CG B:HIS696 4.2 9.3 1.0 CG B:HIS660 4.2 11.8 1.0 ND1 B:HIS696 4.2 12.3 1.0 ND1 B:HIS660 4.2 13.3 1.0 O B:HOH1284 4.3 12.8 1.0 ND1 B:HIS656 4.3 16.9 1.0 O B:HOH1105 4.3 16.5 1.0 CE1 B:HIS656 4.3 11.6 1.0 CB B:ASP697 4.4 11.1 1.0 CB B:ASP808 4.5 12.7 1.0 O B:HOH1457 4.7 11.1 1.0 CG2 B:VAL664 4.8 10.5 1.0 O B:HOH1262 4.9 28.0 1.0 CA B:ASP808 4.9 12.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of of PDE2-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of of PDE2-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:17.2 occ:1.00 OD2 C:ASP697 2.1 11.9 1.0 NE2 C:HIS660 2.1 12.3 1.0 NE2 C:HIS696 2.1 12.3 1.0 OD1 C:ASP808 2.2 16.2 1.0 O C:HOH1425 2.3 12.8 1.0 O C:HOH1107 2.3 15.0 1.0 CD2 C:HIS696 3.0 13.0 1.0 CD2 C:HIS660 3.0 13.6 1.0 CG C:ASP697 3.1 11.7 1.0 CG C:ASP808 3.1 17.7 1.0 CE1 C:HIS660 3.2 12.2 1.0 CE1 C:HIS696 3.2 11.9 1.0 OD2 C:ASP808 3.3 23.0 1.0 OD1 C:ASP697 3.6 9.6 1.0 MG C:MG1002 3.9 13.8 1.0 O C:HOH1122 4.1 13.6 1.0 CD2 C:HIS656 4.1 16.2 1.0 CG C:HIS696 4.2 13.4 1.0 CG C:HIS660 4.2 12.2 1.0 ND1 C:HIS696 4.2 13.4 1.0 ND1 C:HIS660 4.2 13.0 1.0 O C:HOH1102 4.3 17.6 1.0 CB C:ASP697 4.3 12.1 1.0 NE2 C:HIS656 4.3 17.1 1.0 CB C:ASP808 4.5 15.4 1.0 O C:HOH1410 4.7 11.8 1.0 CG2 C:VAL664 4.9 10.4 1.0 CA C:ASP808 5.0 13.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of of PDE2-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of of PDE2-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1001 b:18.1 occ:1.00 OD1 D:ASP808 2.1 16.3 1.0 OD2 D:ASP697 2.1 12.8 1.0 NE2 D:HIS696 2.1 11.1 1.0 NE2 D:HIS660 2.2 12.1 1.0 O D:HOH1176 2.3 16.9 1.0 O D:HOH1120 2.4 17.1 1.0 CD2 D:HIS696 3.0 14.5 1.0 CG D:ASP808 3.1 18.1 1.0 CD2 D:HIS660 3.1 12.9 1.0 CE1 D:HIS696 3.1 13.5 1.0 CG D:ASP697 3.2 12.1 1.0 CE1 D:HIS660 3.2 11.9 1.0 OD2 D:ASP808 3.3 22.3 1.0 OD1 D:ASP697 3.7 12.7 1.0 MG D:MG1002 3.9 14.9 1.0 O D:HOH1429 4.2 13.1 1.0 CG D:HIS696 4.2 12.4 1.0 ND1 D:HIS696 4.2 14.5 1.0 CD2 D:HIS656 4.3 15.5 1.0 ND1 D:HIS660 4.3 13.9 1.0 CG D:HIS660 4.3 12.7 1.0 O D:HOH1113 4.3 20.1 1.0 CB D:ASP697 4.4 12.4 1.0 NE2 D:HIS656 4.4 15.0 1.0 CB D:ASP808 4.5 13.5 1.0 O D:HOH1446 4.7 11.1 1.0 CG2 D:VAL664 4.8 13.9 1.0 CA D:ASP808 5.0 14.9 1.0

M.S.Plummer, J.Cornicelli, H.Roark, D.J.Skalitzky, C.J.Stankovic, S.Bove, J.Pandit, A.Goodman, J.Hicks, A.Shahripour, D.Beidler, X.K.Lu, B.Sanchez, C.Whitehead, R.Sarver, T.Braden, R.Gowan, X.Q.Shen, K.Welch, A.Ogden, N.Sadagopan, H.Baum, H.Miller, C.Banotai, C.Spessard, S.Lightle. Discovery of Potent, Selective, Bioavailable Phosphodiesterase 2 (PDE2) Inhibitors Active in An Osteoarthritis Pain Model, Part I: Transformation of Selective Pyrazolodiazepinone Phosphodiesterase 4 (PDE4) Inhibitors Into Selective PDE2 Inhibitors. Bioorg.Med.Chem.Lett. V. 23 3438 2013.
ISSN: ISSN 0960-894X
PubMed: 23582272
DOI: 10.1016/J.BMCL.2013.03.072