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Zinc in PDB 5edg: Human PDE10A in Complex with 3-(2-Chloro-5-Phenyl-3H-Imidazol-4-Yl)-1- (3-Trifluoromethoxy-Phenyl)-1H-Pyridazin-4-One at 2.30A

Enzymatic activity of Human PDE10A in Complex with 3-(2-Chloro-5-Phenyl-3H-Imidazol-4-Yl)-1- (3-Trifluoromethoxy-Phenyl)-1H-Pyridazin-4-One at 2.30A

All present enzymatic activity of Human PDE10A in Complex with 3-(2-Chloro-5-Phenyl-3H-Imidazol-4-Yl)-1- (3-Trifluoromethoxy-Phenyl)-1H-Pyridazin-4-One at 2.30A:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Human PDE10A in Complex with 3-(2-Chloro-5-Phenyl-3H-Imidazol-4-Yl)-1- (3-Trifluoromethoxy-Phenyl)-1H-Pyridazin-4-One at 2.30A, PDB code: 5edg was solved by C.Joseph, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.47 / 2.30
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.148, 135.148, 235.062, 90.00, 90.00, 120.00
R / Rfree (%) 21.2 / 26.1

Other elements in 5edg:

The structure of Human PDE10A in Complex with 3-(2-Chloro-5-Phenyl-3H-Imidazol-4-Yl)-1- (3-Trifluoromethoxy-Phenyl)-1H-Pyridazin-4-One at 2.30A also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Magnesium (Mg) 4 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human PDE10A in Complex with 3-(2-Chloro-5-Phenyl-3H-Imidazol-4-Yl)-1- (3-Trifluoromethoxy-Phenyl)-1H-Pyridazin-4-One at 2.30A (pdb code 5edg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human PDE10A in Complex with 3-(2-Chloro-5-Phenyl-3H-Imidazol-4-Yl)-1- (3-Trifluoromethoxy-Phenyl)-1H-Pyridazin-4-One at 2.30A, PDB code: 5edg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5edg

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Zinc binding site 1 out of 4 in the Human PDE10A in Complex with 3-(2-Chloro-5-Phenyl-3H-Imidazol-4-Yl)-1- (3-Trifluoromethoxy-Phenyl)-1H-Pyridazin-4-One at 2.30A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human PDE10A in Complex with 3-(2-Chloro-5-Phenyl-3H-Imidazol-4-Yl)-1- (3-Trifluoromethoxy-Phenyl)-1H-Pyridazin-4-One at 2.30A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:33.4
occ:1.00
 OD2 A:ASP564 2.1 24.4 1.0
NE2 A:HIS563 2.1 24.0 1.0
NE2 A:HIS529 2.2 27.6 1.0
OD1 A:ASP674 2.2 36.5 1.0
O A:HOH947 2.2 24.6 1.0
O A:HOH977 2.4 27.0 1.0
CD2 A:HIS563 3.0 23.4 1.0
CE1 A:HIS529 3.0 27.8 1.0
CG A:ASP674 3.1 32.7 1.0
CG A:ASP564 3.1 25.8 1.0
CE1 A:HIS563 3.2 24.8 1.0
CD2 A:HIS529 3.2 27.8 1.0
OD2 A:ASP674 3.3 36.2 1.0
OD1 A:ASP564 3.6 22.2 1.0
MG A:MG802 3.8 25.8 1.0
O A:HOH981 4.1 24.9 1.0
CG A:HIS563 4.2 24.9 1.0
ND1 A:HIS529 4.2 27.6 1.0
CD2 A:HIS525 4.2 30.9 1.0
ND1 A:HIS563 4.2 22.9 1.0
CB A:ASP564 4.3 26.1 1.0
CG A:HIS529 4.3 26.8 1.0
O A:HOH951 4.4 38.9 1.0
CB A:ASP674 4.4 31.0 1.0
O A:HOH911 4.6 24.1 1.0
NE2 A:HIS525 4.6 32.4 1.0
CG2 A:VAL533 4.8 23.6 1.0
CA A:ASP674 4.9 30.5 1.0
O A:ASP674 4.9 31.1 1.0

Zinc binding site 2 out of 4 in 5edg

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Zinc binding site 2 out of 4 in the Human PDE10A in Complex with 3-(2-Chloro-5-Phenyl-3H-Imidazol-4-Yl)-1- (3-Trifluoromethoxy-Phenyl)-1H-Pyridazin-4-One at 2.30A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human PDE10A in Complex with 3-(2-Chloro-5-Phenyl-3H-Imidazol-4-Yl)-1- (3-Trifluoromethoxy-Phenyl)-1H-Pyridazin-4-One at 2.30A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:33.2
occ:1.00
 OD1 B:ASP674 2.1 30.1 1.0
OD2 B:ASP564 2.1 29.8 1.0
NE2 B:HIS563 2.1 24.0 1.0
O B:HOH932 2.2 20.5 1.0
O B:HOH960 2.2 36.7 1.0
NE2 B:HIS529 2.2 27.6 1.0
CG B:ASP674 3.0 31.5 1.0
CG B:ASP564 3.1 29.3 1.0
CD2 B:HIS563 3.1 24.4 1.0
CE1 B:HIS563 3.1 25.4 1.0
CD2 B:HIS529 3.1 29.2 1.0
OD2 B:ASP674 3.2 31.9 1.0
CE1 B:HIS529 3.3 30.4 1.0
OD1 B:ASP564 3.5 26.3 1.0
MG B:MG802 3.8 27.3 1.0
O B:HOH964 3.9 17.5 1.0
CD2 B:HIS525 4.1 31.6 1.0
ND1 B:HIS563 4.2 24.1 1.0
CG B:HIS563 4.2 27.6 1.0
CB B:ASP564 4.3 29.4 1.0
CG B:HIS529 4.3 28.9 1.0
ND1 B:HIS529 4.3 30.3 1.0
O B:HOH930 4.4 34.1 1.0
CB B:ASP674 4.4 31.5 1.0
NE2 B:HIS525 4.4 33.6 1.0
O B:HOH915 4.5 24.2 1.0
CG2 B:VAL533 4.8 27.9 1.0
O B:ASP674 4.8 31.7 1.0
CA B:ASP674 4.9 31.4 1.0

Zinc binding site 3 out of 4 in 5edg

Go back to Zinc Binding Sites List in 5edg
Zinc binding site 3 out of 4 in the Human PDE10A in Complex with 3-(2-Chloro-5-Phenyl-3H-Imidazol-4-Yl)-1- (3-Trifluoromethoxy-Phenyl)-1H-Pyridazin-4-One at 2.30A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human PDE10A in Complex with 3-(2-Chloro-5-Phenyl-3H-Imidazol-4-Yl)-1- (3-Trifluoromethoxy-Phenyl)-1H-Pyridazin-4-One at 2.30A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:32.1
occ:1.00
 O C:HOH945 2.0 32.2 1.0
NE2 C:HIS529 2.1 27.3 1.0
OD2 C:ASP564 2.1 30.3 1.0
OD1 C:ASP674 2.1 30.2 1.0
O C:HOH907 2.1 26.1 1.0
NE2 C:HIS563 2.2 27.4 1.0
CG C:ASP674 2.9 28.7 1.0
CD2 C:HIS563 3.0 27.6 1.0
CE1 C:HIS529 3.0 29.3 1.0
OD2 C:ASP674 3.0 25.8 1.0
CG C:ASP564 3.1 30.6 1.0
CD2 C:HIS529 3.1 27.2 1.0
CE1 C:HIS563 3.3 27.5 1.0
OD1 C:ASP564 3.6 33.0 1.0
MG C:MG802 3.8 26.9 1.0
ND1 C:HIS529 4.2 28.9 1.0
CD2 C:HIS525 4.2 33.7 1.0
O C:HOH971 4.2 37.1 1.0
CG C:HIS563 4.2 27.6 1.0
CG C:HIS529 4.2 28.8 1.0
O C:HOH934 4.3 34.6 1.0
CB C:ASP564 4.3 30.2 1.0
CB C:ASP674 4.3 30.5 1.0
ND1 C:HIS563 4.4 26.7 1.0
O C:HOH923 4.5 29.6 1.0
NE2 C:HIS525 4.6 33.6 1.0
CA C:ASP674 4.8 30.9 1.0
CG2 C:VAL533 4.9 28.7 1.0
O C:ASP674 4.9 32.2 1.0

Zinc binding site 4 out of 4 in 5edg

Go back to Zinc Binding Sites List in 5edg
Zinc binding site 4 out of 4 in the Human PDE10A in Complex with 3-(2-Chloro-5-Phenyl-3H-Imidazol-4-Yl)-1- (3-Trifluoromethoxy-Phenyl)-1H-Pyridazin-4-One at 2.30A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human PDE10A in Complex with 3-(2-Chloro-5-Phenyl-3H-Imidazol-4-Yl)-1- (3-Trifluoromethoxy-Phenyl)-1H-Pyridazin-4-One at 2.30A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:50.5
occ:1.00
 OD2 D:ASP564 2.0 51.5 1.0
NE2 D:HIS563 2.1 43.2 1.0
O D:HOH930 2.2 31.5 1.0
OD1 D:ASP674 2.2 50.7 1.0
NE2 D:HIS529 2.3 48.0 1.0
O D:HOH935 2.3 37.7 1.0
CD2 D:HIS563 2.9 43.6 1.0
CG D:ASP564 3.0 47.0 1.0
CD2 D:HIS529 3.1 48.8 1.0
CG D:ASP674 3.2 50.8 1.0
CE1 D:HIS563 3.2 42.8 1.0
CE1 D:HIS529 3.4 48.2 1.0
OD2 D:ASP674 3.5 51.9 1.0
OD1 D:ASP564 3.5 46.6 1.0
MG D:MG802 3.7 43.5 1.0
O D:HOH903 4.0 52.2 1.0
O D:HOH931 4.1 40.7 1.0
CG D:HIS563 4.1 44.1 1.0
CB D:ASP564 4.2 45.6 1.0
ND1 D:HIS563 4.2 43.2 1.0
CD2 D:HIS525 4.3 52.9 1.0
CG D:HIS529 4.4 47.5 1.0
O D:HOH904 4.4 40.2 1.0
ND1 D:HIS529 4.4 48.1 1.0
CB D:ASP674 4.5 50.6 1.0
NE2 D:HIS525 4.7 52.6 1.0
O D:ASP674 4.8 51.8 1.0
CG2 D:VAL533 4.8 45.5 1.0
CA D:ASP674 5.0 50.8 1.0

Reference:

B.Kuhn, W.Guba, J.Hert, D.Banner, C.Bissantz, S.Ceccarelli, W.Haap, M.Korner, A.Kuglstatter, C.Lerner, P.Mattei, W.Neidhart, E.Pinard, M.G.Rudolph, T.Schulz-Gasch, T.Woltering, M.Stahl. A Real-World Perspective on Molecular Design. J.Med.Chem. V. 59 4087 2016.
ISSN: ISSN 0022-2623
PubMed: 26878596
DOI: 10.1021/ACS.JMEDCHEM.5B01875
Page generated: Sun Oct 27 15:10:09 2024

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