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Magnesium 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
Zinc (Zn) 4 atoms
Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5edg

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:25.8
occ:1.00
 OD1 A:ASP564 1.9 22.2 1.0
O A:HOH981 1.9 24.9 1.0
O A:HOH911 2.1 24.1 1.0
O A:HOH947 2.1 24.6 1.0
O A:HOH924 2.1 23.6 1.0
O A:HOH917 2.2 27.4 1.0
CG A:ASP564 3.0 25.8 1.0
OD2 A:ASP564 3.3 24.4 1.0
ZN A:ZN801 3.8 33.4 1.0
O A:HOH977 4.0 27.0 1.0
NE2 A:HIS595 4.0 31.9 1.0
OE2 A:GLU592 4.1 29.8 1.0
CD2 A:HIS567 4.2 31.2 1.0
O A:HOH982 4.3 33.0 1.0
CD2 A:HIS595 4.4 31.9 1.0
CB A:ASP564 4.4 26.1 1.0
CD2 A:HIS563 4.4 23.4 1.0
NE2 A:HIS567 4.4 34.4 1.0
CD2 A:HIS525 4.5 30.9 1.0
O A:HIS563 4.5 27.1 1.0
OG1 A:THR633 4.5 33.5 1.0
O A:THR633 4.6 31.4 1.0
NE2 A:HIS525 4.7 32.4 1.0
NE2 A:HIS563 4.7 24.0 1.0
OD2 A:ASP674 4.7 36.2 1.0
CA A:ASP564 4.8 26.8 1.0
CD A:GLU592 4.9 29.8 1.0
CB A:THR633 4.9 31.5 1.0
CG A:GLU592 5.0 30.2 1.0

Magnesium binding site 2 out of 4 in 5edg

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:27.3
occ:1.00
 O B:HOH932 1.9 20.5 1.0
O B:HOH964 2.0 17.5 1.0
O B:HOH955 2.0 19.4 1.0
O B:HOH915 2.0 24.2 1.0
OD1 B:ASP564 2.1 26.3 1.0
O B:HOH906 2.1 16.8 1.0
CG B:ASP564 3.1 29.3 1.0
OD2 B:ASP564 3.5 29.8 1.0
ZN B:ZN801 3.8 33.2 1.0
OE2 B:GLU592 4.0 29.9 1.0
NE2 B:HIS595 4.0 34.2 1.0
O B:HOH960 4.1 36.7 1.0
O B:HOH926 4.1 30.0 1.0
CD2 B:HIS567 4.2 29.4 1.0
CD2 B:HIS595 4.3 34.9 1.0
CD2 B:HIS563 4.3 24.4 1.0
NE2 B:HIS567 4.3 30.4 1.0
OG1 B:THR633 4.3 28.9 1.0
CB B:ASP564 4.4 29.4 1.0
OD2 B:ASP674 4.4 31.9 1.0
O B:HIS563 4.5 30.3 1.0
CD2 B:HIS525 4.5 31.6 1.0
NE2 B:HIS525 4.6 33.6 1.0
NE2 B:HIS563 4.6 24.0 1.0
O B:THR633 4.6 30.2 1.0
CA B:ASP564 4.8 29.9 1.0
CB B:THR633 4.8 29.0 1.0
CD B:GLU592 4.8 31.6 1.0
CG B:GLU592 4.9 31.5 1.0

Magnesium binding site 3 out of 4 in 5edg

Go back to Magnesium Binding Sites List in 5edg
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:26.9
occ:1.00
 O C:HOH923 2.0 29.6 1.0
OD1 C:ASP564 2.0 33.0 1.0
O C:HOH956 2.0 29.3 1.0
O C:HOH971 2.0 37.1 1.0
O C:HOH907 2.1 26.1 1.0
O C:HOH939 2.1 25.1 1.0
CG C:ASP564 3.0 30.6 1.0
OD2 C:ASP564 3.4 30.3 1.0
ZN C:ZN801 3.8 32.1 1.0
O C:HOH945 4.0 32.2 1.0
NE2 C:HIS595 4.0 32.3 1.0
OE2 C:GLU592 4.1 32.3 1.0
CD2 C:HIS567 4.1 33.1 1.0
OG1 C:THR633 4.3 27.2 1.0
O C:HIS563 4.3 28.8 1.0
NE2 C:HIS567 4.3 32.8 1.0
CD2 C:HIS595 4.3 31.7 1.0
CD2 C:HIS563 4.3 27.6 1.0
CB C:ASP564 4.4 30.2 1.0
OD2 C:ASP674 4.4 25.8 1.0
O C:HOH954 4.5 49.2 1.0
CA C:ASP564 4.7 30.1 1.0
O C:THR633 4.7 30.2 1.0
NE2 C:HIS563 4.8 27.4 1.0
CB C:THR633 4.8 28.7 1.0
CD2 C:HIS525 4.8 33.7 1.0
CG C:GLU592 4.8 32.4 1.0
CD C:GLU592 4.9 32.1 1.0
NE2 C:HIS525 4.9 33.6 1.0

Magnesium binding site 4 out of 4 in 5edg

Go back to Magnesium Binding Sites List in 5edg
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:43.5
occ:1.00
 O D:HOH931 1.9 40.7 1.0
O D:HOH930 2.0 31.5 1.0
O D:HOH908 2.1 41.1 1.0
O D:HOH929 2.1 36.7 1.0
OD1 D:ASP564 2.2 46.6 1.0
O D:HOH904 2.2 40.2 1.0
CG D:ASP564 3.2 47.0 1.0
OD2 D:ASP564 3.4 51.5 1.0
O D:HOH935 3.6 37.7 1.0
O D:HOH936 3.7 36.5 1.0
ZN D:ZN801 3.7 50.5 1.0
OE2 D:GLU592 3.9 44.5 1.0
CD2 D:HIS567 4.2 49.0 1.0
NE2 D:HIS595 4.3 50.5 1.0
NE2 D:HIS567 4.3 49.8 1.0
OG1 D:THR633 4.3 48.9 1.0
CD2 D:HIS525 4.4 52.9 1.0
O D:THR633 4.4 50.0 1.0
CD2 D:HIS563 4.4 43.6 1.0
NE2 D:HIS525 4.5 52.6 1.0
CB D:ASP564 4.5 45.6 1.0
OD2 D:ASP674 4.6 51.9 1.0
CD2 D:HIS595 4.6 49.4 1.0
O D:HIS563 4.6 44.4 1.0
CB D:THR633 4.8 49.8 1.0
NE2 D:HIS563 4.8 43.2 1.0
CA D:ASP564 4.9 45.4 1.0
CD D:GLU592 4.9 47.9 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: Tue Aug 12 07:41:10 2025

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