3SL6

Crystal structure of the catalytic domain of PDE4D2 with compound 12c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Thiophene inhibitors of PDE4: Crystal structures show a second binding mode at the catalytic domain of PDE4D2.

Nankervis, J.L.Feil, S.C.Hancock, N.C.Zheng, Z.Ng, H.L.Morton, C.J.Holien, J.K.Ho, P.W.Frazzetto, M.M.Jennings, I.G.Manallack, D.T.Martin, T.J.Thompson, P.E.Parker, M.W.

(2011) Bioorg Med Chem Lett 21: 7089-7093

  • DOI: 10.1016/j.bmcl.2011.09.109
  • Primary Citation of Related Structures:  
    3SL4, 3SL5, 3SL6, 3SL8, 3SL3

  • PubMed Abstract: 
  • PDE4 inhibitors have been identified as therapeutic targets for a variety of conditions, particularly inflammatory diseases. We have serendipitously identified a novel class of phosphodiesterase 4 (PDE4) inhibitor during a study to discover antagonists of the parathyroid hormone receptor ...

    PDE4 inhibitors have been identified as therapeutic targets for a variety of conditions, particularly inflammatory diseases. We have serendipitously identified a novel class of phosphodiesterase 4 (PDE4) inhibitor during a study to discover antagonists of the parathyroid hormone receptor. X-ray crystallographic studies of PDE4D2 complexed to four potent inhibitors reveal the atomic details of how they inhibit the enzyme and a notable contrast to another recently reported thiophene-based inhibitor.


    Organizational Affiliation

    Medicinal Chemistry & Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville campus), Parkville, Victoria, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4DA, B, C, D361Homo sapiensMutation(s): 0 
Gene Names: PDE4DDPDE3
EC: 3.1.4.17 (PDB Primary Data), 3.1.4.53 (UniProt)
Find proteins for Q08499 (Homo sapiens)
Explore Q08499 
Go to UniProtKB:  Q08499
NIH Common Fund Data Resources
PHAROS:  Q08499
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JN8
Query on JN8

Download Ideal Coordinates CCD File 
HA [auth C], N [auth A], V [auth B], VA [auth D]cyclopentyl 6-(ethylcarbamoyl)-2-[(thiophen-2-ylacetyl)amino]-4,5,6,7-tetrahydrothieno[2,3-c]pyridine-3-carboxylate
C22 H27 N3 O4 S2
TWWIEHZKMVMPFQ-UHFFFAOYSA-N
 Ligand Interaction
EPE
Query on EPE

Download Ideal Coordinates CCD File 
AA [auth C]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
W [auth B]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], JA [auth D], KA [auth D], Q [auth B], R [auth B], Y [auth C], Z [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth C] , CA [auth C] , DA [auth C] , EA [auth C] , FA [auth C] , G [auth A] , GA [auth C] , H [auth A] , 
BA [auth C],  CA [auth C],  DA [auth C],  EA [auth C],  FA [auth C],  G [auth A],  GA [auth C],  H [auth A],  I [auth A],  IA [auth D],  J [auth A],  K [auth A],  L [auth A],  LA [auth D],  M [auth A],  MA [auth D],  NA [auth D],  O [auth A],  OA [auth D],  P [auth A],  PA [auth D],  QA [auth D],  RA [auth D],  S [auth B],  SA [auth D],  T [auth B],  TA [auth D],  U [auth B],  UA [auth D],  X [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JN8IC50:  290   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.54α = 90
b = 111.2β = 90
c = 160.95γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-06-24 
  • Released Date: 2011-10-26 
  • Deposition Author(s): Feil, S.F.

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2011-12-14
    Changes: Database references