Atomistry » Zinc » PDB 3wym-3zqr » 3wym
Atomistry »
  Zinc »
    PDB 3wym-3zqr »
      3wym »

Zinc in PDB 3wym: Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(1H-Pyrazol-1-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl-1H- Pyrazol-5-Yl)Pyridazin-4(1H)-One

Enzymatic activity of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(1H-Pyrazol-1-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl-1H- Pyrazol-5-Yl)Pyridazin-4(1H)-One

All present enzymatic activity of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(1H-Pyrazol-1-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl-1H- Pyrazol-5-Yl)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 1- (2-Fluoro-4-(1H-Pyrazol-1-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl-1H- Pyrazol-5-Yl)Pyridazin-4(1H)-One, PDB code: 3wym 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) 44.96 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.701, 81.707, 161.533, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 21.5

Other elements in 3wym:

The structure of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(1H-Pyrazol-1-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl-1H- Pyrazol-5-Yl)Pyridazin-4(1H)-One also contains other interesting chemical elements:

Fluorine (F) 2 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 1- (2-Fluoro-4-(1H-Pyrazol-1-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl-1H- Pyrazol-5-Yl)Pyridazin-4(1H)-One (pdb code 3wym). 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 1- (2-Fluoro-4-(1H-Pyrazol-1-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl-1H- Pyrazol-5-Yl)Pyridazin-4(1H)-One, PDB code: 3wym:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3wym

Go back to Zinc Binding Sites List in 3wym
Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(1H-Pyrazol-1-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl-1H- Pyrazol-5-Yl)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 1- (2-Fluoro-4-(1H-Pyrazol-1-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl-1H- Pyrazol-5-Yl)Pyridazin-4(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:24.4
occ:1.00
 OD2 A:ASP554 2.1 17.0 1.0
NE2 A:HIS519 2.2 15.3 1.0
OD1 A:ASP664 2.2 18.5 1.0
O A:HOH1115 2.2 18.2 1.0
NE2 A:HIS553 2.2 16.8 1.0
O A:HOH1125 2.3 16.3 1.0
CD2 A:HIS553 3.1 16.7 1.0
CG A:ASP664 3.1 19.7 1.0
CG A:ASP554 3.1 17.2 1.0
CE1 A:HIS519 3.1 15.4 1.0
CD2 A:HIS519 3.2 15.4 1.0
CE1 A:HIS553 3.3 16.7 1.0
OD2 A:ASP664 3.3 22.1 1.0
OD1 A:ASP554 3.6 17.8 1.0
MG A:MG1001 3.8 17.8 1.0
CD2 A:HIS515 4.0 18.2 1.0
O A:HOH1112 4.0 16.4 1.0
O A:HOH1124 4.2 15.9 1.0
ND1 A:HIS519 4.3 15.8 1.0
NE2 A:HIS515 4.3 18.4 1.0
CG A:HIS553 4.3 17.0 1.0
CB A:ASP554 4.3 17.2 1.0
CG A:HIS519 4.3 16.1 1.0
ND1 A:HIS553 4.3 16.7 1.0
CB A:ASP664 4.5 18.3 1.0
O A:HOH1103 4.7 16.3 1.0
CG2 A:VAL523 4.8 16.9 1.0
CA A:ASP664 4.9 17.2 1.0
O A:ASP664 4.9 16.8 1.0

Zinc binding site 2 out of 2 in 3wym

Go back to Zinc Binding Sites List in 3wym
Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(1H-Pyrazol-1-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl-1H- Pyrazol-5-Yl)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 1- (2-Fluoro-4-(1H-Pyrazol-1-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl-1H- Pyrazol-5-Yl)Pyridazin-4(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:24.2
occ:1.00
 OD2 B:ASP554 2.1 20.4 1.0
OD1 B:ASP664 2.1 19.8 1.0
NE2 B:HIS519 2.2 17.1 1.0
NE2 B:HIS553 2.2 18.4 1.0
O B:HOH1131 2.2 15.3 1.0
O B:HOH1105 2.3 14.7 1.0
CD2 B:HIS553 3.1 18.4 1.0
CG B:ASP664 3.1 20.9 1.0
CG B:ASP554 3.1 20.7 1.0
CE1 B:HIS519 3.1 17.2 1.0
CD2 B:HIS519 3.1 17.0 1.0
CE1 B:HIS553 3.2 18.5 1.0
OD2 B:ASP664 3.4 22.9 1.0
OD1 B:ASP554 3.6 20.7 1.0
MG B:MG1001 3.8 22.1 1.0
O B:HOH1116 4.1 16.9 1.0
CD2 B:HIS515 4.1 21.2 1.0
O B:HOH1107 4.2 17.8 1.0
ND1 B:HIS519 4.2 17.2 1.0
CG B:HIS553 4.3 18.5 1.0
CG B:HIS519 4.3 17.1 1.0
ND1 B:HIS553 4.3 18.4 1.0
CB B:ASP554 4.3 20.3 1.0
NE2 B:HIS515 4.4 21.9 1.0
CB B:ASP664 4.5 19.6 1.0
O B:HOH1104 4.8 17.8 1.0
CG2 B:VAL523 4.8 16.6 1.0
CA B:ASP664 4.8 18.3 1.0
O B:ASP664 4.8 17.6 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 18:25:57 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy