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Zinc 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
Magnesium (Mg) 4 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 5i2r

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Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:40.5
occ:1.00
 OD2 A:ASP564 2.0 33.5 1.0
NE2 A:HIS529 2.2 31.5 1.0
OD1 A:ASP674 2.2 37.9 1.0
O A:HOH975 2.2 25.8 1.0
NE2 A:HIS563 2.2 31.0 1.0
O A:HOH919 2.4 28.9 1.0
CG A:ASP564 3.1 32.5 1.0
CD2 A:HIS563 3.1 31.6 1.0
CG A:ASP674 3.1 35.3 1.0
CE1 A:HIS529 3.1 33.0 1.0
CD2 A:HIS529 3.1 33.0 1.0
CE1 A:HIS563 3.2 31.8 1.0
OD2 A:ASP674 3.3 38.9 1.0
OD1 A:ASP564 3.6 32.2 1.0
MG A:MG802 3.7 22.4 1.0
O A:HOH992 4.0 38.8 1.0
CD2 A:HIS525 4.1 31.1 1.0
ND1 A:HIS529 4.2 33.5 1.0
CG A:HIS563 4.2 31.9 1.0
ND1 A:HIS563 4.2 30.6 1.0
CG A:HIS529 4.3 32.0 1.0
NE2 A:HIS525 4.3 31.3 1.0
CB A:ASP564 4.3 31.8 1.0
O A:HOH916 4.4 35.4 1.0
CB A:ASP674 4.5 34.5 1.0
O A:HOH908 4.5 19.8 1.0
CG2 A:VAL533 4.9 31.9 1.0
CA A:ASP674 4.9 34.4 1.0
O A:ASP674 4.9 34.6 1.0
O A:HOH938 4.9 20.8 1.0

Zinc binding site 2 out of 4 in 5i2r

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Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:34.4
occ:1.00
 OD2 B:ASP564 2.1 28.3 1.0
NE2 B:HIS529 2.2 27.8 1.0
OD1 B:ASP674 2.2 32.8 1.0
NE2 B:HIS563 2.2 31.8 1.0
O B:HOH975 2.3 17.6 1.0
O B:HOH967 2.4 39.3 1.0
CG B:ASP674 3.0 31.1 1.0
CD2 B:HIS563 3.1 30.9 1.0
CE1 B:HIS529 3.1 28.0 1.0
CG B:ASP564 3.2 32.0 1.0
CD2 B:HIS529 3.2 27.3 1.0
OD2 B:ASP674 3.3 30.1 1.0
CE1 B:HIS563 3.3 32.8 1.0
OD1 B:ASP564 3.7 32.5 1.0
O B:HOH994 3.7 24.5 1.0
MG B:MG802 3.8 20.3 1.0
CD2 B:HIS525 4.2 35.5 1.0
ND1 B:HIS529 4.2 29.3 1.0
CG B:HIS563 4.3 31.6 1.0
CG B:HIS529 4.3 29.0 1.0
ND1 B:HIS563 4.3 31.9 1.0
CB B:ASP564 4.4 31.3 1.0
CB B:ASP674 4.4 31.4 1.0
O B:HOH952 4.4 31.0 1.0
NE2 B:HIS525 4.5 33.9 1.0
O B:HOH957 4.7 25.4 1.0
CG2 B:VAL533 4.8 28.4 1.0
O B:ASP674 4.8 30.8 1.0
CA B:ASP674 4.9 31.0 1.0
O B:HOH928 5.0 18.8 1.0

Zinc binding site 3 out of 4 in 5i2r

Go back to Zinc Binding Sites List in 5i2r
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:36.7
occ:1.00
 OD2 C:ASP564 2.0 31.5 1.0
NE2 C:HIS529 2.1 32.9 1.0
OD1 C:ASP674 2.1 33.4 1.0
O C:HOH942 2.2 47.5 1.0
NE2 C:HIS563 2.3 28.4 1.0
O C:HOH974 2.3 22.0 1.0
CG C:ASP674 3.0 33.1 1.0
CE1 C:HIS529 3.1 32.9 1.0
CD2 C:HIS529 3.1 32.7 1.0
CD2 C:HIS563 3.1 26.6 1.0
CG C:ASP564 3.1 31.5 1.0
OD2 C:ASP674 3.3 33.6 1.0
CE1 C:HIS563 3.3 27.5 1.0
OD1 C:ASP564 3.7 30.0 1.0
MG C:MG802 3.8 18.9 1.0
CD2 C:HIS525 4.0 37.2 1.0
ND1 C:HIS529 4.2 32.4 1.0
CG C:HIS529 4.2 31.4 1.0
NE2 C:HIS525 4.2 38.6 1.0
CG C:HIS563 4.3 28.1 1.0
CB C:ASP564 4.3 30.3 1.0
O C:HOH1011 4.3 31.8 1.0
O C:HOH943 4.4 33.6 1.0
CB C:ASP674 4.4 33.0 1.0
ND1 C:HIS563 4.4 25.1 1.0
O C:HOH944 4.6 29.6 1.0
O C:ASP674 4.8 33.4 1.0
CA C:ASP674 4.8 32.9 1.0
CG2 C:VAL533 4.9 29.1 1.0

Zinc binding site 4 out of 4 in 5i2r

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Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:48.7
occ:1.00
 O D:HOH909 2.0 27.8 1.0
OD2 D:ASP564 2.1 42.4 1.0
OD1 D:ASP674 2.1 47.1 1.0
NE2 D:HIS529 2.2 40.0 1.0
NE2 D:HIS563 2.3 39.2 1.0
O D:HOH919 2.6 36.0 1.0
CG D:ASP674 3.1 45.8 1.0
CE1 D:HIS529 3.2 39.1 1.0
CD2 D:HIS563 3.2 38.5 1.0
CD2 D:HIS529 3.2 40.7 1.0
CG D:ASP564 3.2 40.8 1.0
CE1 D:HIS563 3.3 39.1 1.0
OD2 D:ASP674 3.4 47.7 1.0
MG D:MG802 3.6 30.3 1.0
OD1 D:ASP564 3.8 40.3 1.0
O D:HOH925 4.0 35.0 1.0
O D:HOH930 4.2 34.3 1.0
CD2 D:HIS525 4.3 43.0 1.0
ND1 D:HIS529 4.3 40.2 1.0
CG D:HIS529 4.3 40.5 1.0
CG D:HIS563 4.3 40.1 1.0
CB D:ASP564 4.4 40.8 1.0
ND1 D:HIS563 4.4 39.3 1.0
NE2 D:HIS525 4.4 43.6 1.0
CB D:ASP674 4.4 44.9 1.0
O D:ASP674 4.7 45.2 1.0
CG2 D:VAL533 4.7 41.1 1.0
CA D:ASP674 4.8 44.7 1.0
O D:HOH920 5.0 30.1 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 17:47:37 2024

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