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Zinc in PDB 4pm0: PDE7A Catalytic Domain in Complex with 2-(Cyclopentylamino)Thieno[3,2- D]Pyrimidin-4(3H)-One Derivative

Enzymatic activity of PDE7A Catalytic Domain in Complex with 2-(Cyclopentylamino)Thieno[3,2- D]Pyrimidin-4(3H)-One Derivative

All present enzymatic activity of PDE7A Catalytic Domain in Complex with 2-(Cyclopentylamino)Thieno[3,2- D]Pyrimidin-4(3H)-One Derivative:
3.1.4.53;

Protein crystallography data

The structure of PDE7A Catalytic Domain in Complex with 2-(Cyclopentylamino)Thieno[3,2- D]Pyrimidin-4(3H)-One Derivative, PDB code: 4pm0 was solved by K.Kawai, Y.Endo, T.Asano, S.Amano, K.Sawada, N.Ueo, N.Takahashi, Y.Sonoda, N.Kamei, N.Nagata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.75 / 2.10
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 116.187, 116.187, 64.458, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 21.8

Other elements in 4pm0:

The structure of PDE7A Catalytic Domain in Complex with 2-(Cyclopentylamino)Thieno[3,2- D]Pyrimidin-4(3H)-One Derivative also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the PDE7A Catalytic Domain in Complex with 2-(Cyclopentylamino)Thieno[3,2- D]Pyrimidin-4(3H)-One Derivative (pdb code 4pm0). 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 PDE7A Catalytic Domain in Complex with 2-(Cyclopentylamino)Thieno[3,2- D]Pyrimidin-4(3H)-One Derivative, PDB code: 4pm0:

Zinc binding site 1 out of 1 in 4pm0

Go back to Zinc Binding Sites List in 4pm0
Zinc binding site 1 out of 1 in the PDE7A Catalytic Domain in Complex with 2-(Cyclopentylamino)Thieno[3,2- D]Pyrimidin-4(3H)-One Derivative


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PDE7A Catalytic Domain in Complex with 2-(Cyclopentylamino)Thieno[3,2- D]Pyrimidin-4(3H)-One Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:27.6
occ:1.00
 OD2 A:ASP253 2.1 18.9 1.0
OD1 A:ASP362 2.2 18.9 1.0
O A:HOH834 2.2 22.0 1.0
NE2 A:HIS252 2.3 20.7 1.0
NE2 A:HIS216 2.3 19.7 1.0
O A:HOH672 2.4 19.0 1.0
CG A:ASP253 3.0 18.9 1.0
CD2 A:HIS252 3.1 16.6 1.0
CG A:ASP362 3.1 22.8 1.0
CE1 A:HIS216 3.2 20.6 1.0
CD2 A:HIS216 3.3 22.2 1.0
OD2 A:ASP362 3.3 25.3 1.0
CE1 A:HIS252 3.4 18.2 1.0
OD1 A:ASP253 3.5 18.7 1.0
MG A:MG502 3.8 20.2 1.0
O A:HOH673 4.1 21.8 1.0
O A:HOH698 4.2 18.4 1.0
CD2 A:HIS212 4.2 19.6 1.0
CB A:ASP253 4.2 16.2 1.0
NE2 A:HIS212 4.2 22.3 1.0
CG A:HIS252 4.3 15.9 1.0
ND1 A:HIS216 4.3 20.1 1.0
ND1 A:HIS252 4.4 17.8 1.0
CG A:HIS216 4.4 20.8 1.0
CB A:ASP362 4.4 19.3 1.0
CG2 A:VAL220 4.6 17.6 1.0
O A:HOH676 4.7 14.2 1.0
O A:ASP362 4.8 22.6 1.0
CA A:ASP362 4.9 20.3 1.0

Reference:

K.Kawai, Y.Endo, T.Asano, S.Amano, K.Sawada, N.Ueo, N.Takahashi, Y.Sonoda, M.Nagai, N.Kamei, N.Nagata. Discovery of 2-(Cyclopentylamino)Thieno[3,2-D]Pyrimidin-4(3H)-One Derivatives As A New Series of Potent Phosphodiesterase 7 Inhibitors. J.Med.Chem. 2014.
ISSN: ISSN 0022-2623
PubMed: 25383422
DOI: 10.1021/JM5008215
Page generated: Wed Aug 20 21:28:12 2025

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