6C7I

Crystal structure of human phosphodiesterase 2A with 1-(2-chloro-5-methoxy-phenyl)-N-isobutyl-4-methyl-[1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Mathematical and Structural Characterization of Strong Nonadditive Structure-Activity Relationship Caused by Protein Conformational Changes.

Gomez, L.Xu, R.Sinko, W.Selfridge, B.Vernier, W.Ly, K.Truong, R.Metz, M.Marrone, T.Sebring, K.Yan, Y.Appleton, B.Aertgeerts, K.Massari, M.E.Breitenbucher, J.G.

(2018) J Med Chem 61: 7754-7766

  • DOI: 10.1021/acs.jmedchem.8b00713
  • Primary Citation of Related Structures:  
    6C7E, 6C7D, 6C7G, 6C7F, 6C7I, 6C7J

  • PubMed Abstract: 
  • In medicinal chemistry, accurate prediction of additivity-based structure-activity relationship (SAR) analysis rests on three assumptions: (1) a consistent binding pose of the central scaffold, (2) no interaction between the R group substituents, and (3) a relatively rigid binding pocket in which the R group substituents act independently ...

    In medicinal chemistry, accurate prediction of additivity-based structure-activity relationship (SAR) analysis rests on three assumptions: (1) a consistent binding pose of the central scaffold, (2) no interaction between the R group substituents, and (3) a relatively rigid binding pocket in which the R group substituents act independently. Previously, examples of nonadditive SAR have been documented in systems that deviate from the first two assumptions. Local protein structural change upon ligand binding, through induced fit or conformational selection, although a well-known phenomenon that invalidates the third assumption, has not been linked to nonadditive SAR conclusively. Here, for the first time, we present clear structural evidence that the formation of a hydrophobic pocket upon ligand binding in PDE2 catalytic site reduces the size of another distinct subpocket and contributes to strong nonadditive SAR between two otherwise distant R groups.


    Organizational Affiliation

    Dart Neuroscience LLC , 12278 Scripps Summit Drive , San Diego , California 92131 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cGMP-dependent 3',5'-cyclic phosphodiesteraseA, B, C, D342Homo sapiensMutation(s): 0 
Gene Names: PDE2A
EC: 3.1.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for O00408 (Homo sapiens)
Explore O00408 
Go to UniProtKB:  O00408
PHAROS:  O00408
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
EP7 Binding MOAD:  6C7I IC50: 0.38 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.902α = 109.33
b = 72.682β = 91.13
c = 90.816γ = 91.06
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2018-01-22 
  • Released Date: 2018-08-15 
  • Deposition Author(s): Xu, R., Aertgeerts, K.

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection, Database references
  • Version 1.2: 2018-09-26
    Changes: Data collection, Database references