3LY2

Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Water-soluble PDE4 inhibitors for the treatment of dry eye.

Govek, S.P.Oshiro, G.Anzola, J.V.Beauregard, C.Chen, J.Coyle, A.R.Gamache, D.A.Hellberg, M.R.Hsien, J.N.Lerch, J.M.Liao, J.C.Malecha, J.W.Staszewski, L.M.Thomas, D.J.Yanni, J.M.Noble, S.A.Shiau, A.K.

(2010) Bioorg.Med.Chem.Lett. 20: 2928-2932

  • DOI: 10.1016/j.bmcl.2010.03.023

  • PubMed Abstract: 
  • PDE4 inhibitors have the potential to alleviate the symptoms and underlying inflammation associated with dry eye. Disclosed herein is the development of a novel series of water-soluble PDE4 inhibitors. Our studies led to the discovery of coumarin 18, ...

    PDE4 inhibitors have the potential to alleviate the symptoms and underlying inflammation associated with dry eye. Disclosed herein is the development of a novel series of water-soluble PDE4 inhibitors. Our studies led to the discovery of coumarin 18, which is effective in a rabbit model of dry eye and a tear secretion test in rats.


    Organizational Affiliation

    Kalypsys, Inc., 10420 Wateridge Circle, San Diego, CA 92121, United States. sgovek@san.rr.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-specific 3',5'-cyclic phosphodiesterase 4B
A, B, C, D, E, F, G, H
357Homo sapiensMutation(s): 0 
Gene Names: PDE4B (DPDE4)
EC: 3.1.4.53
Find proteins for Q07343 (Homo sapiens)
Go to Gene View: PDE4B
Go to UniProtKB:  Q07343
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Z72
Query on Z72

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
8-(cyclopentyloxy)-4-[(3,5-dichloropyridin-4-yl)amino]-7-methoxy-2H-chromen-2-one
C20 H18 Cl2 N2 O4
YUTTWVBLGONANE-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Z72IC50: 5 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.205 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 214.796α = 90.00
b = 233.964β = 90.00
c = 165.258γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
Blu-Icedata collection
CNXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance