4Y2B

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

• PDB DOI: https://doi.org/10.2210/pdb4Y2B/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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: 2.20 Å
• R-Value Free: 0.196 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 

Starting Model: experimental

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: https://doi.org/10.1016/j.bmcl.2015.03.031
• Primary Citation of Related Structures:  
  4Y2B


• 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. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 44.95 kDa 
• Atom Count: 2,903 
• Modelled Residue Count: 318 
• Deposited Residue Count: 389 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A	A	389	Homo sapiens	Mutation(s): 0  Gene Names: PDE7A EC: 3.1.4.53
UniProt & NIH Common Fund Data Resources
Find proteins for Q13946 (Homo sapiens) Explore Q13946  Go to UniProtKB:  Q13946
PHAROS:  Q13946 GTEx:  ENSG00000205268

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPK	D [auth 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	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.196 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.961	α = 90
b = 115.961	β = 90
c = 64.409	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2015-05-06
  Changes: Database references
• Version 1.3: 2017-10-04
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy
• Version 1.4: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description