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Zinc in PDB 4y2b: Co-Crystal Structure of 3-Ethyl-2-(Isopropylamino)-7-(Pyridin-3-Yl) Thieno[3,2-D]Pyrimidin-4(3H)-One Bound to PDE7A

Enzymatic activity of Co-Crystal Structure of 3-Ethyl-2-(Isopropylamino)-7-(Pyridin-3-Yl) Thieno[3,2-D]Pyrimidin-4(3H)-One Bound to PDE7A

All present enzymatic activity of Co-Crystal Structure of 3-Ethyl-2-(Isopropylamino)-7-(Pyridin-3-Yl) Thieno[3,2-D]Pyrimidin-4(3H)-One Bound to PDE7A:
3.1.4.53;

Protein crystallography data

The structure of Co-Crystal Structure of 3-Ethyl-2-(Isopropylamino)-7-(Pyridin-3-Yl) Thieno[3,2-D]Pyrimidin-4(3H)-One Bound to PDE7A, PDB code: 4y2b was solved by Y.Endo, K.Kawai, T.Asano, S.Amano, Y.Asanuma, K.Sawada, Y.Onodera, N.Ueo, N.Takahashi, Y.Sonoda, N.Kamei, T.Irie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.67 / 2.20
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.961, 115.961, 64.409, 90.00, 90.00, 120.00
R / Rfree (%) 15.8 / 19.6

Other elements in 4y2b:

The structure of Co-Crystal Structure of 3-Ethyl-2-(Isopropylamino)-7-(Pyridin-3-Yl) Thieno[3,2-D]Pyrimidin-4(3H)-One Bound to PDE7A also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Co-Crystal Structure of 3-Ethyl-2-(Isopropylamino)-7-(Pyridin-3-Yl) Thieno[3,2-D]Pyrimidin-4(3H)-One Bound to PDE7A (pdb code 4y2b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Co-Crystal Structure of 3-Ethyl-2-(Isopropylamino)-7-(Pyridin-3-Yl) Thieno[3,2-D]Pyrimidin-4(3H)-One Bound to PDE7A, PDB code: 4y2b:

Zinc binding site 1 out of 1 in 4y2b

Go back to Zinc Binding Sites List in 4y2b
Zinc binding site 1 out of 1 in the Co-Crystal Structure of 3-Ethyl-2-(Isopropylamino)-7-(Pyridin-3-Yl) Thieno[3,2-D]Pyrimidin-4(3H)-One Bound to PDE7A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Co-Crystal Structure of 3-Ethyl-2-(Isopropylamino)-7-(Pyridin-3-Yl) Thieno[3,2-D]Pyrimidin-4(3H)-One Bound to PDE7A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:26.7
occ:1.00
 OD2 A:ASP253 2.1 17.7 1.0
O A:HOH883 2.1 18.6 1.0
NE2 A:HIS252 2.3 16.8 1.0
NE2 A:HIS216 2.3 17.9 1.0
OD1 A:ASP362 2.3 15.4 1.0
O A:HOH686 2.4 16.4 1.0
CD2 A:HIS252 3.0 14.3 1.0
CG A:ASP253 3.0 18.3 1.0
CG A:ASP362 3.2 18.0 1.0
CE1 A:HIS216 3.2 15.4 1.0
CD2 A:HIS216 3.3 16.5 1.0
CE1 A:HIS252 3.4 18.3 1.0
OD2 A:ASP362 3.4 23.0 1.0
OD1 A:ASP253 3.4 16.0 1.0
MG A:MG502 3.6 18.1 1.0
O A:HOH687 3.8 16.9 1.0
O A:HOH713 4.1 16.8 1.0
CG A:HIS252 4.3 16.5 1.0
CB A:ASP253 4.3 14.5 1.0
NE2 A:HIS212 4.3 19.1 1.0
CD2 A:HIS212 4.3 15.3 1.0
ND1 A:HIS216 4.3 17.9 1.0
ND1 A:HIS252 4.4 14.9 1.0
CG A:HIS216 4.4 17.0 1.0
CB A:ASP362 4.5 16.1 1.0
O A:HOH690 4.6 13.5 1.0
CG2 A:VAL220 4.8 15.8 1.0
O A:ASP362 4.8 19.6 1.0
CA A:ASP362 5.0 17.6 1.0

Reference:

Y.Endo, K.Kawai, T.Asano, S.Amano, Y.Asanuma, K.Sawada, Y.Onodera, N.Ueo, N.Takahashi, Y.Sonoda, N.Kamei, T.Irie. 2-(Isopropylamino)Thieno[3,2-D]Pyrimidin-4(3H)-One Derivatives As Selective Phosphodiesterase 7 Inhibitors with Potent in Vivo Efficacy Bioorg.Med.Chem.Lett. 2015.
ISSN: ESSN 1464-3405
DOI: 10.1016/J.BMCL.2015.03.031
Page generated: Wed Dec 16 05:55:57 2020

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