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

Go back to Magnesium Binding Sites List in 5i2r
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

Go back to Magnesium Binding Sites List in 5i2r
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

Go back to Magnesium Binding Sites List in 5i2r
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: Mon Dec 14 20:29:17 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy