Zinc in PDB 4mvh: 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: 4mvh 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)	24.38 / 2.50
Space group	F 2 3
Cell size a, b, c (Å), α, β, γ (°)	252.062, 252.062, 252.062, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 18.2

The binding sites of Zinc atom in the Crystal Structure of PDE10A with Novel Keto-Benzimidazole Inhibitor (pdb code 4mvh). 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: 4mvh:
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:42.2 occ:1.00 OD2 A:ASP554 2.0 32.2 1.0 OD1 A:ASP664 2.3 33.9 1.0 NE2 A:HIS519 2.4 34.9 1.0 NE2 A:HIS553 2.4 31.8 1.0 CG A:ASP554 3.0 31.4 1.0 CD2 A:HIS519 3.1 34.9 1.0 CG A:ASP664 3.1 34.4 1.0 CD2 A:HIS553 3.2 31.0 1.0 OD2 A:ASP664 3.3 35.7 1.0 CE1 A:HIS553 3.5 31.8 1.0 OD1 A:ASP554 3.5 32.4 1.0 ZN A:ZN1002 3.5 54.6 1.0 CE1 A:HIS519 3.5 35.5 1.0 CD2 A:HIS515 4.0 39.0 1.0 CB A:ASP554 4.2 32.2 1.0 O A:HOH1140 4.2 50.0 1.0 NE2 A:HIS515 4.4 40.2 1.0 CG A:HIS553 4.4 31.3 1.0 CG A:HIS519 4.4 35.2 1.0 ND1 A:HIS553 4.5 31.5 1.0 ND1 A:HIS519 4.5 36.1 1.0 CB A:ASP664 4.5 35.1 1.0 CG2 A:VAL523 4.9 32.9 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:54.6 occ:1.00 OD1 A:ASP554 2.1 32.4 1.0 CG A:ASP554 3.0 31.4 1.0 OD2 A:ASP554 3.3 32.2 1.0 ZN A:ZN1001 3.5 42.2 1.0 OE2 A:GLU582 4.1 34.7 1.0 NE2 A:HIS585 4.1 31.1 1.0 O A:HOH1140 4.1 50.0 1.0 OG1 A:THR623 4.2 34.4 1.0 O A:HOH1165 4.3 27.1 1.0 CD2 A:HIS553 4.3 31.0 1.0 O A:HIS553 4.4 30.6 1.0 OD2 A:ASP664 4.4 35.7 1.0 CB A:ASP554 4.4 32.2 1.0 CD2 A:HIS557 4.4 38.4 1.0 CD2 A:HIS585 4.4 30.8 1.0 O A:THR623 4.5 35.1 1.0 NE2 A:HIS557 4.5 38.5 1.0 CB A:THR623 4.6 34.0 1.0 NE2 A:HIS515 4.7 40.2 1.0 NE2 A:HIS553 4.7 31.8 1.0 CD2 A:HIS515 4.8 39.0 1.0 CA A:ASP554 4.8 32.4 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:42.9 occ:1.00 OD2 B:ASP554 2.1 31.8 1.0 OD1 B:ASP664 2.1 40.5 1.0 NE2 B:HIS553 2.5 30.3 1.0 NE2 B:HIS519 2.5 34.0 1.0 O B:HOH901 2.7 40.7 1.0 CG B:ASP664 2.9 39.5 1.0 OD2 B:ASP664 3.0 40.3 1.0 CG B:ASP554 3.1 32.1 1.0 CD2 B:HIS553 3.2 29.9 1.0 CD2 B:HIS519 3.4 32.9 1.0 ZN B:ZN802 3.4 53.4 1.0 CE1 B:HIS519 3.5 33.7 1.0 OD1 B:ASP554 3.5 31.8 1.0 CE1 B:HIS553 3.5 30.6 1.0 CD2 B:HIS515 4.1 37.2 1.0 CB B:ASP664 4.3 39.4 1.0 CB B:ASP554 4.3 32.5 1.0 CG B:HIS553 4.4 30.5 1.0 NE2 B:HIS515 4.5 37.9 1.0 ND1 B:HIS553 4.5 30.6 1.0 ND1 B:HIS519 4.6 33.2 1.0 CG B:HIS519 4.6 32.6 1.0 CG2 B:VAL523 4.9 32.9 1.0 CA B:ASP664 4.9 38.7 1.0 O B:ASP664 4.9 40.5 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:53.4 occ:1.00 OD1 B:ASP554 2.1 31.8 1.0 O B:HOH927 2.2 33.6 1.0 CG B:ASP554 3.1 32.1 1.0 OD2 B:ASP554 3.3 31.8 1.0 ZN B:ZN801 3.4 42.9 1.0 O B:HOH901 4.0 40.7 1.0 OE2 B:GLU582 4.1 36.3 1.0 NE2 B:HIS585 4.2 33.7 1.0 OD2 B:ASP664 4.2 40.3 1.0 O B:HIS553 4.3 31.4 1.0 OG1 B:THR623 4.3 35.7 1.0 CD2 B:HIS553 4.3 29.9 1.0 CD2 B:HIS585 4.4 34.0 1.0 CD2 B:HIS557 4.4 38.6 1.0 NE2 B:HIS557 4.4 38.8 1.0 O B:THR623 4.5 35.2 1.0 CB B:ASP554 4.5 32.5 1.0 CB B:THR623 4.6 35.4 1.0 CD2 B:HIS515 4.6 37.2 1.0 NE2 B:HIS553 4.7 30.3 1.0 NE2 B:HIS515 4.8 37.9 1.0 CA B:ASP554 4.8 32.6 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