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Magnesium in PDB 5i2r: Human PDE10A in Complex with 3-(2-Phenylpyrazol-3-Yl)-1-[3- (Trifluoromethoxy)Phenyl]Pyridazin-4-One

Enzymatic activity of Human PDE10A in Complex with 3-(2-Phenylpyrazol-3-Yl)-1-[3- (Trifluoromethoxy)Phenyl]Pyridazin-4-One

All present enzymatic activity of Human PDE10A in Complex with 3-(2-Phenylpyrazol-3-Yl)-1-[3- (Trifluoromethoxy)Phenyl]Pyridazin-4-One:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Human PDE10A in Complex with 3-(2-Phenylpyrazol-3-Yl)-1-[3- (Trifluoromethoxy)Phenyl]Pyridazin-4-One, PDB code: 5i2r was solved by C.Joseph, M.Koerner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.44 / 2.50
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.809, 135.809, 234.864, 90.00, 90.00, 120.00
R / Rfree (%) 19.1 / 25

Other elements in 5i2r:

The structure of Human PDE10A in Complex with 3-(2-Phenylpyrazol-3-Yl)-1-[3- (Trifluoromethoxy)Phenyl]Pyridazin-4-One also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human PDE10A in Complex with 3-(2-Phenylpyrazol-3-Yl)-1-[3- (Trifluoromethoxy)Phenyl]Pyridazin-4-One (pdb code 5i2r). 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-Phenylpyrazol-3-Yl)-1-[3- (Trifluoromethoxy)Phenyl]Pyridazin-4-One, PDB code: 5i2r:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5i2r

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Magnesium binding site 1 out of 4 in the Human PDE10A in Complex with 3-(2-Phenylpyrazol-3-Yl)-1-[3- (Trifluoromethoxy)Phenyl]Pyridazin-4-One


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-Phenylpyrazol-3-Yl)-1-[3- (Trifluoromethoxy)Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:22.4
occ:1.00
 O A:HOH992 1.8 38.8 1.0
OD1 A:ASP564 2.0 32.2 1.0
O A:HOH908 2.0 19.8 1.0
O A:HOH938 2.1 20.8 1.0
O A:HOH990 2.1 27.0 1.0
O A:HOH975 2.2 25.8 1.0
CG A:ASP564 3.0 32.5 1.0
OD2 A:ASP564 3.3 33.5 1.0
O A:HOH922 3.7 38.3 1.0
ZN A:ZN801 3.7 40.5 1.0
OE2 A:GLU592 3.9 34.1 1.0
NE2 A:HIS595 3.9 33.9 1.0
CD2 A:HIS567 4.1 35.0 1.0
O A:HOH919 4.1 28.9 1.0
NE2 A:HIS567 4.3 35.0 1.0
CB A:ASP564 4.3 31.8 1.0
CD2 A:HIS525 4.3 31.1 1.0
CD2 A:HIS595 4.3 33.9 1.0
NE2 A:HIS525 4.4 31.3 1.0
OG1 A:THR633 4.4 38.1 1.0
CD2 A:HIS563 4.5 31.6 1.0
O A:HIS563 4.6 33.2 1.0
O A:THR633 4.6 35.9 1.0
OD2 A:ASP674 4.7 38.9 1.0
NE2 A:HIS563 4.7 31.0 1.0
CB A:THR633 4.7 36.1 1.0
CA A:ASP564 4.8 32.6 1.0
CD A:GLU592 4.9 36.1 1.0
CE1 A:HIS595 5.0 32.1 1.0
CG A:GLU592 5.0 35.9 1.0

Magnesium binding site 2 out of 4 in 5i2r

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Magnesium binding site 2 out of 4 in the Human PDE10A in Complex with 3-(2-Phenylpyrazol-3-Yl)-1-[3- (Trifluoromethoxy)Phenyl]Pyridazin-4-One


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-Phenylpyrazol-3-Yl)-1-[3- (Trifluoromethoxy)Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:20.3
occ:1.00
 O B:HOH928 1.9 18.8 1.0
O B:HOH994 1.9 24.5 1.0
O B:HOH975 1.9 17.6 1.0
O B:HOH957 1.9 25.4 1.0
OD1 B:ASP564 2.0 32.5 1.0
O B:HOH972 2.1 27.9 1.0
CG B:ASP564 3.0 32.0 1.0
OD2 B:ASP564 3.4 28.3 1.0
ZN B:ZN801 3.8 34.4 1.0
OE2 B:GLU592 3.9 31.0 1.0
O B:HOH967 4.0 39.3 1.0
NE2 B:HIS595 4.0 32.7 1.0
CD2 B:HIS567 4.2 35.0 1.0
CD2 B:HIS563 4.3 30.9 1.0
CD2 B:HIS595 4.3 33.5 1.0
NE2 B:HIS567 4.3 32.9 1.0
OG1 B:THR633 4.3 30.0 1.0
O B:THR633 4.4 29.6 1.0
CB B:ASP564 4.4 31.3 1.0
CD2 B:HIS525 4.5 35.5 1.0
O B:HIS563 4.5 31.8 1.0
NE2 B:HIS525 4.6 33.9 1.0
OD2 B:ASP674 4.6 30.1 1.0
NE2 B:HIS563 4.6 31.8 1.0
CB B:THR633 4.7 30.2 1.0
CA B:ASP564 4.7 31.9 1.0
CD B:GLU592 4.8 34.5 1.0
CG B:GLU592 4.9 35.2 1.0

Magnesium binding site 3 out of 4 in 5i2r

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Magnesium binding site 3 out of 4 in the Human PDE10A in Complex with 3-(2-Phenylpyrazol-3-Yl)-1-[3- (Trifluoromethoxy)Phenyl]Pyridazin-4-One


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-Phenylpyrazol-3-Yl)-1-[3- (Trifluoromethoxy)Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:18.9
occ:1.00
 O C:HOH974 1.8 22.0 1.0
O C:HOH944 1.9 29.6 1.0
OD1 C:ASP564 2.0 30.0 1.0
O C:HOH1011 2.1 31.8 1.0
O C:HOH985 2.1 28.5 1.0
O C:HOH928 2.1 20.7 1.0
CG C:ASP564 3.0 31.5 1.0
OD2 C:ASP564 3.4 31.5 1.0
ZN C:ZN801 3.8 36.7 1.0
OE2 C:GLU592 3.9 35.2 1.0
NE2 C:HIS595 4.0 35.8 1.0
OG1 C:THR633 4.1 28.8 1.0
CD2 C:HIS567 4.2 36.0 1.0
CD2 C:HIS563 4.2 26.6 1.0
CD2 C:HIS595 4.3 35.9 1.0
O C:HIS563 4.3 31.0 1.0
O C:HOH940 4.3 31.1 1.0
NE2 C:HIS567 4.3 36.1 1.0
O C:HOH942 4.3 47.5 1.0
CB C:ASP564 4.4 30.3 1.0
O C:THR633 4.4 31.9 1.0
OD2 C:ASP674 4.5 33.6 1.0
CG C:GLU592 4.6 37.1 1.0
NE2 C:HIS525 4.6 38.6 1.0
NE2 C:HIS563 4.7 28.4 1.0
CD C:GLU592 4.7 36.7 1.0
CB C:THR633 4.7 30.8 1.0
CA C:ASP564 4.7 30.8 1.0
CD2 C:HIS525 4.7 37.2 1.0

Magnesium binding site 4 out of 4 in 5i2r

Go back to Magnesium Binding Sites List in 5i2r
Magnesium binding site 4 out of 4 in the Human PDE10A in Complex with 3-(2-Phenylpyrazol-3-Yl)-1-[3- (Trifluoromethoxy)Phenyl]Pyridazin-4-One


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-Phenylpyrazol-3-Yl)-1-[3- (Trifluoromethoxy)Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:30.3
occ:1.00
 O D:HOH909 1.9 27.8 1.0
O D:HOH903 1.9 24.1 1.0
O D:HOH920 2.0 30.1 1.0
O D:HOH917 2.1 23.3 1.0
OD1 D:ASP564 2.1 40.3 1.0
O D:HOH925 2.2 35.0 1.0
CG D:ASP564 2.9 40.8 1.0
OD2 D:ASP564 3.1 42.4 1.0
ZN D:ZN801 3.6 48.7 1.0
O D:HOH919 3.8 36.0 1.0
O D:HOH940 3.8 41.6 1.0
OG1 D:THR633 3.9 41.0 1.0
OE2 D:GLU592 4.0 43.0 1.0
CD2 D:HIS563 4.0 38.5 1.0
OD2 D:ASP674 4.1 47.7 1.0
O D:THR633 4.2 42.7 1.0
O D:HIS563 4.3 40.1 1.0
NE2 D:HIS595 4.3 47.0 1.0
CB D:ASP564 4.3 40.8 1.0
NE2 D:HIS563 4.4 39.2 1.0
CB D:THR633 4.4 42.0 1.0
CD2 D:HIS595 4.5 45.9 1.0
CD2 D:HIS567 4.5 45.2 1.0
NE2 D:HIS525 4.5 43.6 1.0
CD2 D:HIS525 4.5 43.0 1.0
NE2 D:HIS567 4.7 44.4 1.0
CA D:ASP564 4.7 41.1 1.0
OD1 D:ASP674 4.8 47.1 1.0
CG D:ASP674 4.9 45.8 1.0
CD D:GLU592 4.9 43.3 1.0
C D:THR633 5.0 42.8 1.0
C D:HIS563 5.0 40.7 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 Sep 29 16:38:31 2024

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