3SL5

Crystal structure of the catalytic domain of PDE4D2 complexed with compound 10d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1016/j.bmcl.2011.09.109
  • Primary Citation of Related Structures:  
    3SL3, 3SL4, 3SL5, 3SL6, 3SL8

  • 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. 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4D
A, B, C, D
359Homo sapiensMutation(s): 0 
Gene Names: DPDE3PDE4D
EC: 3.1.4.17 (PDB Primary Data), 3.1.4.53 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q08499 (Homo sapiens)
Explore Q08499 
Go to UniProtKB:  Q08499
PHAROS:  Q08499
GTEx:  ENSG00000113448 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08499
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J25
Query on J25

Download Ideal Coordinates CCD File 
CA [auth D],
G [auth A],
M [auth B],
S [auth C]
diethyl 2-[(thiophen-2-ylacetyl)amino]-4,7-dihydrothieno[2,3-c]pyridine-3,6(5H)-dicarboxylate
C19 H22 N2 O5 S2
ZDMGIZFQKKDWAO-UHFFFAOYSA-N
EPE
Query on EPE

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

Download Ideal Coordinates CCD File 
I [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
E [auth A]
F [auth A]
K [auth B]
AA [auth D],
BA [auth D],
E [auth A],
F [auth A],
K [auth B],
L [auth B],
Q [auth C],
R [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
DA [auth D]
EA [auth D]
FA [auth D]
GA [auth D]
H [auth A]
DA [auth D],
EA [auth D],
FA [auth D],
GA [auth D],
H [auth A],
HA [auth D],
IA [auth D],
J [auth A],
N [auth B],
O [auth B],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth D],
Z [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
J25 PDBBind:  3SL5 IC50: 22 (nM) from 1 assay(s)
BindingDB:  3SL5 IC50: 22 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.394α = 90
b = 109.966β = 90
c = 159.613γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • 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
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations