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Magnesium in PDB 5b4l: Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with 1-(Cyclopropylmethyl)-5-(2-(2,3-Dihydro-1H-Imidazo[1,2- A]Benzimidazol-1-Yl)Ethoxy)-3-(1-Phenyl-1H-Pyrazol-5-Yl)Pyridazin- 4(1H)-One

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with 1-(Cyclopropylmethyl)-5-(2-(2,3-Dihydro-1H-Imidazo[1,2- A]Benzimidazol-1-Yl)Ethoxy)-3-(1-Phenyl-1H-Pyrazol-5-Yl)Pyridazin- 4(1H)-One

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with 1-(Cyclopropylmethyl)-5-(2-(2,3-Dihydro-1H-Imidazo[1,2- A]Benzimidazol-1-Yl)Ethoxy)-3-(1-Phenyl-1H-Pyrazol-5-Yl)Pyridazin- 4(1H)-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with 1-(Cyclopropylmethyl)-5-(2-(2,3-Dihydro-1H-Imidazo[1,2- A]Benzimidazol-1-Yl)Ethoxy)-3-(1-Phenyl-1H-Pyrazol-5-Yl)Pyridazin- 4(1H)-One, PDB code: 5b4l 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) 79.59 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.126, 81.537, 159.182, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 28.2

Other elements in 5b4l:

The structure of Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with 1-(Cyclopropylmethyl)-5-(2-(2,3-Dihydro-1H-Imidazo[1,2- A]Benzimidazol-1-Yl)Ethoxy)-3-(1-Phenyl-1H-Pyrazol-5-Yl)Pyridazin- 4(1H)-One also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with 1-(Cyclopropylmethyl)-5-(2-(2,3-Dihydro-1H-Imidazo[1,2- A]Benzimidazol-1-Yl)Ethoxy)-3-(1-Phenyl-1H-Pyrazol-5-Yl)Pyridazin- 4(1H)-One (pdb code 5b4l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with 1-(Cyclopropylmethyl)-5-(2-(2,3-Dihydro-1H-Imidazo[1,2- A]Benzimidazol-1-Yl)Ethoxy)-3-(1-Phenyl-1H-Pyrazol-5-Yl)Pyridazin- 4(1H)-One, PDB code: 5b4l:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5b4l

Go back to Magnesium Binding Sites List in 5b4l
Magnesium binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with 1-(Cyclopropylmethyl)-5-(2-(2,3-Dihydro-1H-Imidazo[1,2- A]Benzimidazol-1-Yl)Ethoxy)-3-(1-Phenyl-1H-Pyrazol-5-Yl)Pyridazin- 4(1H)-One


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with 1-(Cyclopropylmethyl)-5-(2-(2,3-Dihydro-1H-Imidazo[1,2- A]Benzimidazol-1-Yl)Ethoxy)-3-(1-Phenyl-1H-Pyrazol-5-Yl)Pyridazin- 4(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:28.1
occ:1.00
 O A:HOH1120 2.0 32.4 1.0
OD1 A:ASP554 2.1 31.9 1.0
O A:HOH1135 2.1 27.2 1.0
O A:HOH1118 2.1 25.0 1.0
O A:HOH1101 2.2 34.1 1.0
O A:HOH1114 2.2 22.0 1.0
CG A:ASP554 3.1 32.8 1.0
OD2 A:ASP554 3.6 33.2 1.0
OE2 A:GLU582 3.6 52.2 1.0
ZN A:ZN1002 3.8 41.9 1.0
NE2 A:HIS585 3.8 41.4 1.0
CD2 A:HIS515 4.1 39.3 1.0
O A:HOH1104 4.1 27.6 1.0
NE2 A:HIS515 4.1 39.2 1.0
CD2 A:HIS585 4.1 42.2 1.0
CD2 A:HIS557 4.2 39.1 1.0
O A:HIS553 4.3 36.4 1.0
O A:HOH1122 4.3 49.4 1.0
CD2 A:HIS553 4.4 33.3 1.0
NE2 A:HIS557 4.4 38.7 1.0
CB A:ASP554 4.4 33.5 1.0
O A:HOH1140 4.6 45.5 1.0
O A:HOH1141 4.6 53.1 1.0
OG1 A:THR623 4.7 38.8 1.0
CD A:GLU582 4.7 50.8 1.0
OD2 A:ASP664 4.7 40.8 1.0
NE2 A:HIS553 4.7 33.6 1.0
CA A:ASP554 4.7 34.9 1.0
O A:THR623 4.8 39.0 1.0
CE1 A:HIS585 5.0 43.6 1.0
CG A:GLU582 5.0 49.7 1.0
O A:HOH1113 5.0 48.8 1.0

Magnesium binding site 2 out of 2 in 5b4l

Go back to Magnesium Binding Sites List in 5b4l
Magnesium binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with 1-(Cyclopropylmethyl)-5-(2-(2,3-Dihydro-1H-Imidazo[1,2- A]Benzimidazol-1-Yl)Ethoxy)-3-(1-Phenyl-1H-Pyrazol-5-Yl)Pyridazin- 4(1H)-One


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with 1-(Cyclopropylmethyl)-5-(2-(2,3-Dihydro-1H-Imidazo[1,2- A]Benzimidazol-1-Yl)Ethoxy)-3-(1-Phenyl-1H-Pyrazol-5-Yl)Pyridazin- 4(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1001

b:48.0
occ:1.00
 O B:HOH1121 1.9 25.4 1.0
O B:HOH1104 1.9 26.2 1.0
O B:HOH1102 2.1 33.6 1.0
O B:HOH1113 2.2 38.6 1.0
OD1 B:ASP554 2.2 36.8 1.0
O B:HOH1131 2.7 29.3 1.0
CG B:ASP554 3.2 37.0 1.0
OD2 B:ASP554 3.4 36.1 1.0
OE2 B:GLU582 3.6 47.5 1.0
ZN B:ZN1002 3.8 38.8 1.0
NE2 B:HIS585 4.1 43.6 1.0
O B:HIS553 4.1 40.8 1.0
O B:HOH1106 4.1 31.4 1.0
OG1 B:THR623 4.2 42.4 1.0
CD2 B:HIS553 4.2 34.5 1.0
CD2 B:HIS585 4.2 43.7 1.0
O B:THR623 4.4 41.9 1.0
OD2 B:ASP664 4.4 40.0 1.0
CD2 B:HIS557 4.4 38.9 1.0
CB B:ASP554 4.5 37.5 1.0
CD B:GLU582 4.5 47.1 1.0
NE2 B:HIS557 4.6 39.0 1.0
CG B:GLU582 4.6 47.2 1.0
NE2 B:HIS553 4.6 33.9 1.0
NE2 B:HIS515 4.6 42.9 1.0
CB B:THR623 4.7 41.0 1.0
CD2 B:HIS515 4.8 41.4 1.0
CA B:ASP554 4.8 38.6 1.0
O B:HOH1135 4.8 43.3 1.0
C B:HIS553 5.0 38.6 1.0

Reference:

M.Yoshikawa, T.Hitaka, T.Hasui, M.Fushimi, J.Kunitomo, H.Kokubo, H.Oki, K.Nakashima, T.Taniguchi. Design and Synthesis of Potent and Selective Pyridazin-4(1H)-One-Based PDE10A Inhibitors Interacting with TYR683 in the PDE10A Selectivity Pocket Bioorg.Med.Chem. V. 24 3447 2016.
ISSN: ESSN 1464-3391
PubMed: 27301679
DOI: 10.1016/J.BMC.2016.05.049
Page generated: Sun Sep 29 01:01:12 2024

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