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Zinc 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:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5b4l

Go back to Zinc Binding Sites List in 5b4l
Zinc 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 Zinc with other atoms in the Zn 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:Zn1002

b:41.9
occ:1.00
 NE2 A:HIS553 2.0 33.6 1.0
OD2 A:ASP554 2.0 33.2 1.0
OD1 A:ASP664 2.1 39.1 1.0
O A:HOH1104 2.1 27.6 1.0
O A:HOH1120 2.2 32.4 1.0
NE2 A:HIS519 2.3 39.7 1.0
CD2 A:HIS553 2.9 33.3 1.0
CG A:ASP664 2.9 39.8 1.0
OD2 A:ASP664 3.0 40.8 1.0
CG A:ASP554 3.1 32.8 1.0
CE1 A:HIS553 3.1 33.7 1.0
CE1 A:HIS519 3.3 40.2 1.0
CD2 A:HIS519 3.3 41.1 1.0
OD1 A:ASP554 3.5 31.9 1.0
MG A:MG1001 3.8 28.1 1.0
O A:HOH1111 4.0 45.7 1.0
CG A:HIS553 4.1 33.5 1.0
ND1 A:HIS553 4.1 33.0 1.0
CD2 A:HIS515 4.1 39.3 1.0
O A:HOH1101 4.3 34.1 1.0
CB A:ASP554 4.3 33.5 1.0
CB A:ASP664 4.3 39.8 1.0
NE2 A:HIS515 4.4 39.2 1.0
ND1 A:HIS519 4.4 40.0 1.0
O A:HOH1114 4.4 22.0 1.0
CG A:HIS519 4.4 40.4 1.0
O A:HOH1135 4.7 27.2 1.0
CG2 A:VAL523 4.8 35.0 1.0
CA A:ASP664 4.8 39.1 1.0
O A:ASP664 4.9 40.9 1.0
O A:HOH1140 4.9 45.5 1.0

Zinc binding site 2 out of 2 in 5b4l

Go back to Zinc Binding Sites List in 5b4l
Zinc 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 Zinc with other atoms in the Zn 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:Zn1002

b:38.8
occ:1.00
 NE2 B:HIS553 2.0 33.9 1.0
OD2 B:ASP554 2.0 36.1 1.0
NE2 B:HIS519 2.1 35.9 1.0
OD1 B:ASP664 2.2 36.9 1.0
O B:HOH1121 2.3 25.4 1.0
O B:HOH1106 2.4 31.4 1.0
CD2 B:HIS553 2.9 34.5 1.0
CE1 B:HIS553 3.0 33.8 1.0
CE1 B:HIS519 3.0 37.1 1.0
CG B:ASP554 3.1 37.0 1.0
CG B:ASP664 3.2 40.0 1.0
CD2 B:HIS519 3.2 36.0 1.0
OD2 B:ASP664 3.5 40.0 1.0
OD1 B:ASP554 3.7 36.8 1.0
MG B:MG1001 3.8 48.0 1.0
O B:HOH1107 4.0 33.0 1.0
CG B:HIS553 4.0 35.1 1.0
ND1 B:HIS553 4.1 34.5 1.0
CD2 B:HIS515 4.1 41.4 1.0
O B:HOH1131 4.1 29.3 1.0
ND1 B:HIS519 4.2 36.7 1.0
CB B:ASP554 4.2 37.5 1.0
CG B:HIS519 4.3 36.3 1.0
NE2 B:HIS515 4.3 42.9 1.0
CB B:ASP664 4.5 40.7 1.0
O B:HOH1102 4.6 33.6 1.0
CG2 B:VAL523 4.8 34.2 1.0
CA B:ASP664 4.8 40.8 1.0
O B:ASP664 4.9 42.6 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 Oct 27 13:20:31 2024

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