Zinc in PDB 4muw: Crystal Structure of PDE10A with Novel Keto-Benzimidazole Inhibitor

All present enzymatic activity of Crystal Structure of PDE10A with Novel Keto-Benzimidazole Inhibitor:
3.1.4.17; 3.1.4.35;

The structure of Crystal Structure of PDE10A with Novel Keto-Benzimidazole Inhibitor, PDB code: 4muw was solved by S.Chmait, S.Jordan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.19 / 2.64
Space group	F 2 3
Cell size a, b, c (Å), α, β, γ (°)	252.659, 252.659, 252.659, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 19.6

The structure of Crystal Structure of PDE10A with Novel Keto-Benzimidazole Inhibitor also contains other interesting chemical elements:

Fluorine

(F)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE10A with Novel Keto-Benzimidazole Inhibitor (pdb code 4muw). 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 PDE10A with Novel Keto-Benzimidazole Inhibitor, PDB code: 4muw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of PDE10A with Novel Keto-Benzimidazole Inhibitor


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 PDE10A with Novel Keto-Benzimidazole Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:51.9 occ:1.00 OD2 A:ASP554 2.0 44.8 1.0 OD1 A:ASP664 2.1 44.9 1.0 NE2 A:HIS553 2.4 36.7 1.0 NE2 A:HIS519 2.5 42.7 1.0 CG A:ASP554 3.1 41.5 1.0 CG A:ASP664 3.1 45.1 1.0 CD2 A:HIS553 3.2 37.1 1.0 OD2 A:ASP664 3.3 44.9 1.0 ZN A:ZN1002 3.3 56.3 1.0 CD2 A:HIS519 3.4 42.4 1.0 CE1 A:HIS519 3.4 43.5 1.0 CE1 A:HIS553 3.4 37.2 1.0 OD1 A:ASP554 3.5 42.2 1.0 CD2 A:HIS515 3.8 44.5 1.0 O A:HOH1104 4.0 39.4 1.0 NE2 A:HIS515 4.1 46.0 1.0 CB A:ASP554 4.4 39.6 1.0 CG A:HIS553 4.4 36.9 1.0 ND1 A:HIS519 4.5 45.6 1.0 CB A:ASP664 4.5 46.2 1.0 CG A:HIS519 4.5 43.5 1.0 ND1 A:HIS553 4.5 37.5 1.0 O A:HOH1170 4.7 37.6 1.0 O A:ASP664 4.9 47.8 1.0 CG2 A:VAL523 4.9 35.5 1.0 CA A:ASP664 4.9 47.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of PDE10A with Novel Keto-Benzimidazole Inhibitor


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 PDE10A with Novel Keto-Benzimidazole Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:56.3 occ:1.00 OD1 A:ASP554 2.1 42.2 1.0 O A:HOH1170 2.4 37.6 1.0 O A:HOH1172 2.4 35.8 1.0 O A:HOH1171 2.5 40.4 1.0 O A:HOH1104 2.5 39.4 1.0 CG A:ASP554 3.1 41.5 1.0 OD2 A:ASP554 3.3 44.8 1.0 ZN A:ZN1001 3.3 51.9 1.0 OE2 A:GLU582 4.1 39.8 1.0 OG1 A:THR623 4.1 40.6 1.0 CD2 A:HIS553 4.2 37.1 1.0 NE2 A:HIS585 4.2 40.9 1.0 OD2 A:ASP664 4.3 44.9 1.0 CD2 A:HIS515 4.4 44.5 1.0 O A:HIS553 4.4 36.4 1.0 O A:HOH1174 4.4 36.4 1.0 CB A:ASP554 4.4 39.6 1.0 NE2 A:HIS515 4.5 46.0 1.0 NE2 A:HIS553 4.5 36.7 1.0 CD2 A:HIS585 4.5 40.1 1.0 O A:THR623 4.5 38.8 1.0 CB A:THR623 4.6 37.4 1.0 CD2 A:HIS557 4.6 41.1 1.0 OD1 A:ASP664 4.8 44.9 1.0 CA A:ASP554 4.9 39.3 1.0 NE2 A:HIS557 4.9 42.6 1.0 O A:HOH1179 4.9 43.6 1.0 CG A:ASP664 5.0 45.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of PDE10A with Novel Keto-Benzimidazole Inhibitor


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 PDE10A with Novel Keto-Benzimidazole Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:50.7 occ:1.00 OD1 B:ASP664 2.0 43.2 1.0 OD2 B:ASP554 2.3 41.0 1.0 NE2 B:HIS553 2.3 33.6 1.0 NE2 B:HIS519 2.6 43.3 1.0 O B:HOH970 2.6 48.3 1.0 CG B:ASP664 2.9 42.6 1.0 OD2 B:ASP664 3.1 41.9 1.0 CG B:ASP554 3.2 38.0 1.0 CD2 B:HIS553 3.2 34.0 1.0 ZN B:ZN802 3.3 61.3 1.0 CE1 B:HIS553 3.3 33.4 1.0 OD1 B:ASP554 3.4 37.3 1.0 CE1 B:HIS519 3.5 43.0 1.0 CD2 B:HIS519 3.6 41.7 1.0 CD2 B:HIS515 3.9 47.7 1.0 O B:HOH904 4.0 41.5 1.0 NE2 B:HIS515 4.1 49.8 1.0 CB B:ASP664 4.2 42.7 1.0 CG B:HIS553 4.3 33.1 1.0 ND1 B:HIS553 4.4 32.3 1.0 CB B:ASP554 4.5 38.4 1.0 O B:HOH914 4.5 42.6 1.0 ND1 B:HIS519 4.6 42.0 1.0 CG B:HIS519 4.7 40.9 1.0 CA B:ASP664 4.8 42.7 1.0 O B:ASP664 4.9 42.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of PDE10A with Novel Keto-Benzimidazole Inhibitor


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 PDE10A with Novel Keto-Benzimidazole Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:61.3 occ:1.00 OD1 B:ASP554 2.2 37.3 1.0 O B:HOH969 2.2 37.6 1.0 O B:HOH914 2.3 42.6 1.0 O B:HOH904 2.4 41.5 1.0 CG B:ASP554 3.2 38.0 1.0 ZN B:ZN801 3.3 50.7 1.0 OD2 B:ASP554 3.5 41.0 1.0 OE2 B:GLU582 3.9 43.4 1.0 OG1 B:THR623 4.1 44.2 1.0 O B:HOH970 4.2 48.3 1.0 OD2 B:ASP664 4.2 41.9 1.0 CD2 B:HIS553 4.2 34.0 1.0 NE2 B:HIS585 4.3 45.7 1.0 O B:HIS553 4.3 35.8 1.0 NE2 B:HIS553 4.4 33.6 1.0 O B:THR623 4.4 42.2 1.0 CD2 B:HIS557 4.4 42.7 1.0 CB B:THR623 4.5 43.5 1.0 NE2 B:HIS515 4.5 49.8 1.0 CB B:ASP554 4.5 38.4 1.0 CD2 B:HIS585 4.5 46.4 1.0 NE2 B:HIS557 4.6 43.5 1.0 CD2 B:HIS515 4.6 47.7 1.0 OD1 B:ASP664 4.8 43.2 1.0 O B:HOH974 4.9 41.3 1.0 CG B:ASP664 4.9 42.6 1.0 CD B:GLU582 4.9 42.7 1.0 CA B:ASP554 4.9 37.7 1.0

E.Hu, R.K.Kunz, N.Chen, S.Rumfelt, A.Siegmund, K.Andrews, S.Chmait, S.Zhao, C.Davis, H.Chen, D.Lester-Zeiner, J.Ma, C.Biorn, J.Shi, A.Porter, J.Treanor, J.R.Allen. Design, Optimization, and Biological Evaluation of Novel Keto-Benzimidazoles As Potent and Selective Inhibitors of Phosphodiesterase 10A (PDE10A). J.Med.Chem. V. 56 8781 2013.
ISSN: ISSN 0022-2623
PubMed: 24102193
DOI: 10.1021/JM401234W