Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44953.31 
• Atom Count: 2619 
• Residue Count: 389 
• Unique protein chains: 1

4Y2B

Co-crystal structure of 3-ethyl-2-(isopropylamino)-7-(pyridin-3-yl)thieno[3,2-d]pyrimidin-4(3H)-one bound to PDE7A

• DOI: 10.2210/pdb4Y2B/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2015-02-09 Released: 2015-04-08 
• Deposition Author(s): Endo, Y., Kawai, K., Asano, T., Amano, S., Asanuma, Y., Sawada, K., Onodera, Y., Ueo, N., Takahashi, N., Sonoda, Y., Kamei, N., Irie, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.196 
• R-Value Work: 0.158 

Literature

2-(Isopropylamino)thieno[3,2-d]pyrimidin-4(3H)-one derivatives as selective phosphodiesterase 7 inhibitors with potent in vivo efficacy

Endo, Y., Kawai, K., Asano, T., Amano, S., Asanuma, Y., Sawada, K., Onodera, Y., Ueo, N., Takahashi, N., Sonoda, Y., Kamei, N., Irie, T.

(2015) Bioorg.Med.Chem.Lett. 25: 1910-1914

• PubMed: 25866242 
• DOI: 10.1016/j.bmcl.2015.03.031


• PubMed Abstract: 
  

A new series of thienopyrimidinones is synthesized and evaluated as selective phosphodiesterase 7 (PDE7) inhibitors for the treatment of inflammatory diseases. The modification of the substituents on thienopyrimidinone revealed that an isopropylamino group at the 2-position was favorable for aqueous solubility. The introduction of 3-pyrrolidines at the 7-position resulted in good solubility, highly potent activity, and good PDE7 selectivity. Among the synthesized compounds, compound 46 exhibited the greatest inhibition of ear edema in a phorbol ester-induced mouse model.

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Organizational Affiliation: 

Drug Research Center, Kaken Pharmaceutical Co. Ltd, 14, Shinomiya Minamigawara-cho, Yamashina, Kyoto 607-8042, Japan.,Drug Research Center, Kaken Pharmaceutical Co. Ltd, 14, Shinomiya Minamigawara-cho, Yamashina, Kyoto 607-8042, Japan. Electronic address: [e-mail].,Department of Clinical Chemistry and Informatics, Kumamoto University, 5-1, Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A	A	389	Homo sapiens	Mutation(s): 0  Gene Names: PDE7A EC: 3.1.4.53
Find proteins for Q13946 (Homo sapiens) Go to Gene View: PDE7A Go to UniProtKB:  Q13946

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EPK	A	3-ethyl-2-(propan-2-ylamino)-7-(pyridin-3-yl)thieno[3,2-d]pyrimidin-4(3H)-one C16 H18 N4 O S TZXUAKHZPAHOMA-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
EPK	IC50: 4.4 nM (100) BINDINGDB
EPK	IC50: 4.4 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.196 
• R-Value Work: 0.158 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 115.961	α = 90.00
b = 115.961	β = 90.00
c = 64.409	γ = 120.00

Software Package:

Software Name	Purpose
HKL-2000	data scaling
HKL-2000	data reduction
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-02-09 
• Released Date: 2015-04-08 
• Deposition Author(s): Endo, Y., Kawai, K., Asano, T., Amano, S., Asanuma, Y., Sawada, K., Onodera, Y., Ueo, N., Takahashi, N., Sonoda, Y., Kamei, N., Irie, T.

Revision History 

• Version 1.0: 2015-04-08
  Type: Initial release
• Version 1.1: 2015-04-29
  Type: Database references
• Version 1.2: 2015-05-06
  Type: Database references
• Version 1.3: 2017-10-04
  Type: Data collection, Database references, Derived calculations, Source and taxonomy