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Zinc in PDB 5axp: Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-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-(2-Oxo-1,3-Oxazolidin-3-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-(2-Oxo-1,3-Oxazolidin-3-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-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One, PDB code: 5axp was solved by H.Oki, Y.Zama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.753, 81.849, 159.684, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 23.4

Other elements in 5axp:

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

Zinc binding site 1 out of 2 in 5axp

Go back to Zinc Binding Sites List in 5axp
Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-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-(2-Oxo-1,3-Oxazolidin-3-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:32.8
occ:1.00
 OD2 A:ASP554 2.1 24.8 1.0
NE2 A:HIS553 2.2 26.8 1.0
OD1 A:ASP664 2.2 25.4 1.0
NE2 A:HIS519 2.2 24.6 1.0
O A:HOH1108 2.3 23.8 1.0
O A:HOH1155 2.4 27.1 1.0
CD2 A:HIS553 3.0 23.4 1.0
CG A:ASP664 3.1 29.1 1.0
CG A:ASP554 3.2 26.0 1.0
CD2 A:HIS519 3.2 24.5 1.0
CE1 A:HIS553 3.2 24.6 1.0
CE1 A:HIS519 3.2 22.8 1.0
OD2 A:ASP664 3.3 35.6 1.0
OD1 A:ASP554 3.6 24.3 1.0
MG A:MG1001 3.8 28.5 1.0
CD2 A:HIS515 4.0 29.2 1.0
O A:HOH1178 4.1 27.2 1.0
O A:HOH1141 4.1 25.3 1.0
CG A:HIS553 4.2 26.6 1.0
ND1 A:HIS553 4.3 24.2 1.0
ND1 A:HIS519 4.3 26.3 1.0
CG A:HIS519 4.3 24.0 1.0
NE2 A:HIS515 4.4 30.7 1.0
CB A:ASP554 4.4 25.2 1.0
CB A:ASP664 4.5 21.7 1.0
O A:HOH1228 4.6 53.1 1.0
CG2 A:VAL523 4.8 18.9 1.0
O A:HOH1104 4.8 26.9 1.0
CA A:ASP664 4.8 23.6 1.0
O A:ASP664 4.9 25.2 1.0

Zinc binding site 2 out of 2 in 5axp

Go back to Zinc Binding Sites List in 5axp
Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-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-(2-Oxo-1,3-Oxazolidin-3-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:31.0
occ:1.00
 OD2 B:ASP554 2.1 27.0 1.0
NE2 B:HIS553 2.1 23.4 1.0
OD1 B:ASP664 2.2 24.7 1.0
O B:HOH1124 2.2 22.1 1.0
NE2 B:HIS519 2.2 25.3 1.0
O B:HOH1138 2.4 30.3 1.0
CD2 B:HIS553 3.0 24.0 1.0
CG B:ASP664 3.1 32.0 1.0
CD2 B:HIS519 3.1 25.6 1.0
CG B:ASP554 3.1 27.5 1.0
CE1 B:HIS553 3.2 22.0 1.0
CE1 B:HIS519 3.2 25.7 1.0
OD2 B:ASP664 3.3 39.0 1.0
OD1 B:ASP554 3.6 25.1 1.0
MG B:MG1001 3.8 28.3 1.0
O B:HOH1171 4.0 28.1 1.0
CD2 B:HIS515 4.1 30.4 1.0
O B:HOH1132 4.2 25.3 1.0
CG B:HIS553 4.2 25.1 1.0
ND1 B:HIS553 4.2 22.8 1.0
CG B:HIS519 4.3 25.5 1.0
ND1 B:HIS519 4.3 22.7 1.0
NE2 B:HIS515 4.3 30.4 1.0
CB B:ASP554 4.4 24.7 1.0
CB B:ASP664 4.4 30.3 1.0
O B:HOH1109 4.7 27.2 1.0
CG2 B:VAL523 4.8 22.6 1.0
CA B:ASP664 4.8 24.6 1.0
O B:ASP664 4.9 25.4 1.0

Reference:

M.Yoshikawa, H.Kamisaki, J.Kunitomo, H.Oki, H.Kokubo, A.Suzuki, T.Ikemoto, K.Nakashima, N.Kamiguchi, A.Harada, H.Kimura, T.Taniguchi. Design and Synthesis of A Novel 2-Oxindole Scaffold As A Highly Potent and Brain-Penetrant Phosphodiesterase 10A Inhibitor Bioorg.Med.Chem. V. 23 7138 2015.
ISSN: ESSN 1464-3391
PubMed: 26494583
DOI: 10.1016/J.BMC.2015.10.002
Page generated: Sun Oct 27 13:14:14 2024

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