Atomistry » Magnesium » PDB 5avz-5bjo » 5b4l
Atomistry »
  Magnesium »
    PDB 5avz-5bjo »
      5b4l »

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

Last articles

Mg in 3WQP
Mg in 3WQY
Mg in 3WQT
Mg in 3WQU
Mg in 3WQL
Mg in 3WQR
Mg in 3WQS
Mg in 3WQD
Mg in 3WQQ
Mg in 3WQE
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy