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Zinc in PDB 3wyl: Crystal Structure of the Catalytic Domain of PDE10A Complexed with 5- Methoxy-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 5- Methoxy-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 5- Methoxy-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 5- Methoxy-3-(1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl) Pyridazin-4(1H)-One, PDB code: 3wyl 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) 37.71 / 2.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.881, 81.833, 162.156, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 26.1

Other elements in 3wyl:

The structure of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 5- Methoxy-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 5- Methoxy-3-(1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl) Pyridazin-4(1H)-One (pdb code 3wyl). 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 5- Methoxy-3-(1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl) Pyridazin-4(1H)-One, PDB code: 3wyl:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3wyl

Go back to Zinc Binding Sites List in 3wyl
Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 5- Methoxy-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 5- Methoxy-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:Zn1001

b:46.9
occ:1.00
 O A:HOH1116 2.0 38.7 1.0
OD2 A:ASP554 2.1 35.9 1.0
NE2 A:HIS553 2.1 32.7 1.0
O A:HOH1107 2.2 32.0 1.0
OD1 A:ASP664 2.2 42.3 1.0
NE2 A:HIS519 2.4 32.5 1.0
CD2 A:HIS553 3.0 33.5 1.0
CE1 A:HIS553 3.1 32.7 1.0
CG A:ASP554 3.1 33.2 1.0
CG A:ASP664 3.1 43.8 1.0
CE1 A:HIS519 3.3 32.9 1.0
OD2 A:ASP664 3.4 50.7 1.0
CD2 A:HIS519 3.4 34.1 1.0
OD1 A:ASP554 3.6 32.2 1.0
MG A:MG1002 3.7 30.3 1.0
O A:HOH1102 3.8 33.6 1.0
O A:HOH1109 3.8 40.8 1.0
CD2 A:HIS515 4.0 46.0 1.0
CG A:HIS553 4.2 33.1 1.0
ND1 A:HIS553 4.2 32.9 1.0
NE2 A:HIS515 4.3 46.5 1.0
CB A:ASP554 4.3 33.8 1.0
ND1 A:HIS519 4.4 34.2 1.0
CB A:ASP664 4.5 41.2 1.0
CG A:HIS519 4.5 32.7 1.0
O A:HOH1108 4.6 27.6 1.0
O A:HOH1103 4.7 22.2 1.0
CG2 A:VAL523 4.9 29.9 1.0
CA A:ASP664 4.9 38.1 1.0
O A:ASP664 5.0 39.4 1.0

Zinc binding site 2 out of 2 in 3wyl

Go back to Zinc Binding Sites List in 3wyl
Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 5- Methoxy-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 5- Methoxy-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:Zn1001

b:42.1
occ:1.00
 O B:HOH1112 2.0 34.9 1.0
NE2 B:HIS553 2.1 43.5 1.0
OD2 B:ASP554 2.2 29.6 1.0
OD1 B:ASP664 2.3 40.7 1.0
NE2 B:HIS519 2.3 33.6 1.0
O B:HOH1104 2.5 62.7 1.0
CD2 B:HIS553 2.8 42.1 1.0
OD2 B:ASP664 2.9 46.7 1.0
CG B:ASP664 2.9 43.4 1.0
CG B:ASP554 3.1 31.4 1.0
CE1 B:HIS519 3.2 32.9 1.0
CE1 B:HIS553 3.2 42.9 1.0
CD2 B:HIS519 3.4 34.2 1.0
OD1 B:ASP554 3.5 30.3 1.0
MG B:MG1002 3.7 43.9 1.0
CG B:HIS553 4.0 42.4 1.0
O B:HOH1110 4.1 50.9 1.0
CD2 B:HIS515 4.1 53.6 1.0
ND1 B:HIS553 4.2 42.7 1.0
CB B:ASP664 4.4 42.7 1.0
ND1 B:HIS519 4.4 33.2 1.0
CB B:ASP554 4.4 32.8 1.0
CG B:HIS519 4.5 33.2 1.0
NE2 B:HIS515 4.6 55.3 1.0
O B:HOH1111 4.6 45.8 1.0
CA B:ASP664 4.9 42.5 1.0
CG2 B:VAL523 4.9 29.3 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 18:24:27 2024

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