4Y8C

Crystal structure of phosphodiesterase 9 in complex with (S)-C33


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Asymmetry of Phosphodiesterase-9A and a Unique Pocket for Selective Binding of a Potent Enantiomeric Inhibitor.

Huang, M.Shao, Y.Hou, J.Cui, W.Liang, B.Huang, Y.Li, Z.Wu, Y.Zhu, X.Liu, P.Wan, Y.Ke, H.Luo, H.B.

(2015) Mol.Pharmacol. 88: 836-845

  • DOI: 10.1124/mol.115.099747
  • Primary Citation of Related Structures:  4Y86, 4Y87

  • PubMed Abstract: 
  • Phosphodiesterase-9 (PDE9) inhibitors have been studied as potential therapeutics for treatment of central nervous system diseases and diabetes. Here, we report the discovery of a new category of PDE9 inhibitors by rational design on the basis of the ...

    Phosphodiesterase-9 (PDE9) inhibitors have been studied as potential therapeutics for treatment of central nervous system diseases and diabetes. Here, we report the discovery of a new category of PDE9 inhibitors by rational design on the basis of the crystal structures. The best compound, (S)-6-((1-(4-chlorophenyl)ethyl)amino)-1-cyclopentyl-1,5,6,7-tetrahydro-4H-pyrazolo[3,4-day]pyrimidin-4-one [(S)-C33], has an IC50 value of 11 nM against PDE9 and the racemic C33 has bioavailability of 56.5% in the rat pharmacokinetic model. The crystal structures of PDE9 in the complex with racemic C33, (R)-C33, and (S)-C33 reveal subtle conformational asymmetry of two M-loops in the PDE9 dimer and different conformations of two C33 enantiomers. The structures also identified a small hydrophobic pocket that interacts with the tyrosyl tail of (S)-C33 but not with (R)-C33, and is thus possibly useful for improvement of selectivity of PDE9 inhibitors. The asymmetry of the M-loop and the different interactions of the C33 enantiomers imply the necessity to consider the whole PDE9 dimer in the design of inhibitors.


    Organizational Affiliation

    School of Chemistry and Chemical Engineering (M.H., J.H., X.Z. Yiq.W.), School of Pharmaceutical Sciences (Y.S., Z.L., Yin.W., P.L., H.-B.L.), Sun Yat-Sen University, Guangzhou, PR China; and Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina (W.C., B.L., Y.H., H.K.).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
A, B
533Homo sapiensGene Names: PDE9A
EC: 3.1.4.35
Find proteins for O76083 (Homo sapiens)
Go to Gene View: PDE9A
Go to UniProtKB:  O76083
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
49D
Query on 49D

Download SDF File 
Download CCD File 
A, B
6-{[(1S)-1-(4-chlorophenyl)ethyl]amino}-1-cyclopentyl-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
C18 H20 Cl N5 O
FIUCLBJMUGCQTF-NSHDSACASA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.205 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 104.719α = 90.00
b = 104.719β = 90.00
c = 270.274γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
AMoREphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-02-16 
  • Released Date: 2015-09-16 
  • Deposition Author(s): Huang, M.

Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM59791

Revision History 

  • Version 1.0: 2015-09-16
    Type: Initial release
  • Version 1.1: 2015-10-14
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations