Atomistry » Zinc » PDB 3wod-3wyl » 3wyk
Atomistry »
  Zinc »
    PDB 3wod-3wyl »
      3wyk »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy