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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

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