4Y2B

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


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

    Department of Clinical Chemistry and Informatics, Kumamoto University, 5-1, Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7AA389Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13946
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPK
Query on EPK

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EPK BindingDB:  4Y2B IC50: 4.4 (nM) from 1 assay(s)
Binding MOAD:  4Y2B IC50: 4.4 (nM) from 1 assay(s)
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 = 115.961α = 90
b = 115.961β = 90
c = 64.409γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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