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Zinc in PDB 4wn1: Crystal Structure of PDE10A in Complex with 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(1H)-One

Enzymatic activity of Crystal Structure of PDE10A in Complex with 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(1H)-One

All present enzymatic activity of Crystal Structure of PDE10A in Complex with 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(1H)-One:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of PDE10A in Complex with 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(1H)-One, PDB code: 4wn1 was solved by Y.Amano, K.Honbou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.61 / 3.13
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.294, 81.727, 159.210, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 32

Other elements in 4wn1:

The structure of Crystal Structure of PDE10A in Complex with 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(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 PDE10A in Complex with 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(1H)-One (pdb code 4wn1). 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 PDE10A in Complex with 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(1H)-One, PDB code: 4wn1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4wn1

Go back to Zinc Binding Sites List in 4wn1
Zinc binding site 1 out of 2 in the Crystal Structure of PDE10A in Complex with 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(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 PDE10A in Complex with 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:26.1
occ:1.00
 O A:HOH906 2.0 20.9 1.0
OD1 A:ASP674 2.3 25.2 1.0
OD2 A:ASP564 2.3 27.3 1.0
NE2 A:HIS563 2.4 38.2 1.0
NE2 A:HIS529 2.4 24.4 1.0
O A:HOH904 2.9 6.2 1.0
CD2 A:HIS563 3.1 37.2 1.0
CG A:ASP674 3.1 25.9 1.0
MG A:MG802 3.2 21.8 1.0
OD2 A:ASP674 3.2 25.5 1.0
CD2 A:HIS529 3.3 23.6 1.0
CG A:ASP564 3.3 27.7 1.0
CE1 A:HIS529 3.4 24.4 1.0
CE1 A:HIS563 3.5 37.5 1.0
O A:HOH901 3.7 4.6 1.0
OD1 A:ASP564 3.7 26.7 1.0
O A:HOH903 3.8 14.2 1.0
CD2 A:HIS525 4.1 35.9 1.0
CG A:HIS563 4.3 36.0 1.0
CG A:HIS529 4.4 23.2 1.0
ND1 A:HIS529 4.4 24.1 1.0
NE2 A:HIS525 4.5 36.0 1.0
ND1 A:HIS563 4.5 38.0 1.0
CB A:ASP674 4.5 26.5 1.0
CB A:ASP564 4.6 28.4 1.0
O A:HOH902 4.9 21.1 1.0
CG2 A:VAL533 4.9 22.7 1.0
CA A:ASP674 4.9 28.5 1.0
O A:ASP674 5.0 29.4 1.0

Zinc binding site 2 out of 2 in 4wn1

Go back to Zinc Binding Sites List in 4wn1
Zinc binding site 2 out of 2 in the Crystal Structure of PDE10A in Complex with 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(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 PDE10A in Complex with 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:22.0
occ:1.00
 O B:HOH908 1.9 31.7 1.0
NE2 B:HIS563 1.9 14.1 1.0
NE2 B:HIS529 2.1 15.5 1.0
OD1 B:ASP674 2.1 12.1 1.0
O B:HOH907 2.2 9.3 1.0
OD2 B:ASP564 2.3 12.4 1.0
CD2 B:HIS563 2.9 14.0 1.0
CE1 B:HIS529 2.9 15.8 1.0
CE1 B:HIS563 3.0 14.0 1.0
CG B:ASP674 3.0 12.3 1.0
OD2 B:ASP674 3.2 12.4 1.0
CG B:ASP564 3.3 12.9 1.0
CD2 B:HIS529 3.3 16.0 1.0
O B:HOH902 3.3 12.5 1.0
MG B:MG802 3.4 13.5 1.0
OD1 B:ASP564 3.8 12.5 1.0
O B:HOH901 4.0 9.2 1.0
CG B:HIS563 4.0 13.9 1.0
ND1 B:HIS563 4.0 13.8 1.0
ND1 B:HIS529 4.1 16.1 1.0
O B:HOH903 4.3 6.9 1.0
CB B:ASP564 4.3 13.7 1.0
CG B:HIS529 4.3 16.6 1.0
CD2 B:HIS525 4.4 32.1 1.0
CB B:ASP674 4.4 12.7 1.0
O B:ASP674 4.8 12.8 1.0
CG2 B:VAL533 4.8 13.2 1.0
CA B:ASP674 4.8 12.9 1.0
O B:HOH905 4.9 8.0 1.0
NE2 B:HIS525 5.0 31.8 1.0

Reference:

W.Hamaguchi, N.Masuda, S.Miyamoto, Y.Shiina, S.Kikuchi, T.Mihara, H.Moriguchi, H.Fushiki, Y.Murakami, Y.Amano, K.Honbou, K.Hattori. Synthesis, Sar Study, and Biological Evaluation of Novel Quinoline Derivatives As Phosphodiesterase 10A Inhibitors with Reduced CYP3A4 Inhibition. Bioorg.Med.Chem. V. 23 297 2015.
ISSN: ESSN 1464-3391
PubMed: 25515954
DOI: 10.1016/J.BMC.2014.11.039
Page generated: Sun Oct 27 09:58:20 2024

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