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Zinc in PDB 3wyk: Crystal Structure of the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(1H)-One

Enzymatic activity of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(1H)-One

All present enzymatic activity of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(1H)-One:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(1H)-One, PDB code: 3wyk was solved by H.Oki, Y.Hayano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.49 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.696, 81.696, 161.192, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 25

Other elements in 3wyk:

The structure of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(1H)-One also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(1H)-One (pdb code 3wyk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(1H)-One, PDB code: 3wyk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3wyk

Go back to Zinc Binding Sites List in 3wyk
Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(1H)-One


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:35.3
occ:1.00
 OD1 A:ASP664 2.1 33.4 1.0
NE2 A:HIS553 2.1 27.1 1.0
O A:HOH1149 2.1 32.4 1.0
NE2 A:HIS519 2.2 30.4 1.0
O A:HOH1168 2.3 32.5 1.0
OD2 A:ASP554 2.3 29.1 1.0
CG A:ASP664 3.0 33.3 1.0
CD2 A:HIS553 3.0 27.5 1.0
CE1 A:HIS519 3.1 29.8 1.0
CE1 A:HIS553 3.1 27.1 1.0
OD2 A:ASP664 3.2 35.1 1.0
CD2 A:HIS519 3.3 30.3 1.0
CG A:ASP554 3.3 29.5 1.0
OD1 A:ASP554 3.7 30.0 1.0
MG A:MG1001 3.9 31.2 1.0
CD2 A:HIS515 4.1 30.7 1.0
O A:HOH1103 4.1 34.2 1.0
CG A:HIS553 4.2 27.7 1.0
ND1 A:HIS553 4.2 27.4 1.0
O A:HOH1169 4.2 24.8 1.0
ND1 A:HIS519 4.2 30.2 1.0
CG A:HIS519 4.3 30.4 1.0
CB A:ASP664 4.4 31.9 1.0
NE2 A:HIS515 4.4 30.8 1.0
CB A:ASP554 4.4 30.2 1.0
O A:HOH1171 4.5 25.1 1.0
O A:ASP664 4.7 32.4 1.0
CA A:ASP664 4.8 30.7 1.0
CG2 A:VAL523 4.8 28.4 1.0
O A:HOH1144 4.9 25.2 1.0

Zinc binding site 2 out of 2 in 3wyk

Go back to Zinc Binding Sites List in 3wyk
Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(1H)-One


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:34.7
occ:1.00
 OD1 B:ASP664 2.1 33.5 1.0
OD2 B:ASP554 2.1 31.6 1.0
NE2 B:HIS553 2.1 31.0 1.0
NE2 B:HIS519 2.2 30.5 1.0
O B:HOH1163 2.2 25.4 1.0
O B:HOH1162 2.4 34.7 1.0
CD2 B:HIS553 3.0 31.3 1.0
CG B:ASP664 3.0 33.7 1.0
CD2 B:HIS519 3.1 30.7 1.0
CG B:ASP554 3.1 32.1 1.0
CE1 B:HIS519 3.2 30.3 1.0
CE1 B:HIS553 3.2 30.9 1.0
OD2 B:ASP664 3.3 34.5 1.0
OD1 B:ASP554 3.5 32.2 1.0
MG B:MG1001 3.9 27.8 1.0
CD2 B:HIS515 4.1 31.6 1.0
O B:HOH1164 4.1 29.9 1.0
CG B:HIS553 4.2 31.6 1.0
ND1 B:HIS553 4.2 30.7 1.0
CG B:HIS519 4.3 30.8 1.0
ND1 B:HIS519 4.3 30.5 1.0
O B:HOH1116 4.3 38.6 1.0
NE2 B:HIS515 4.4 31.9 1.0
CB B:ASP554 4.4 32.3 1.0
CB B:ASP664 4.4 33.0 1.0
O B:HOH1113 4.7 33.8 1.0
CA B:ASP664 4.8 32.2 1.0
CG2 B:VAL523 4.8 25.9 1.0
O B:ASP664 4.9 32.1 1.0

Reference:

J.Kunitomo, M.Yoshikawa, M.Fushimi, A.Kawada, F.J.Quinn, H.Oki, H.Kokubo, M.Kondo, K.Nakashima, N.Kamiguchi, K.Suzuki, H.Kimura, T.Taniguchi. Discovery of 1‑[2-Fluoro-4-(1H‑Pyrazol-1-Yl)Phenyl]-5- Methoxy-3-(1-Pheny‑1H‑Pyrazol-5-Yl)Pyridazin- 4(1H)‑One (Tak-063), A Highly Potent, Selective, and Orally Active Phosphodiesterase 10A (PDE10A)Inhibitor J.Med.Chem. 2014.
ISSN: ISSN 0022-2623
DOI: 10.1021/JM5013648
Page generated: Sat Oct 26 18:23:21 2024

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