Catalytic Domain Of Human Phosphodiesterase 4D In Complex With Roflumilast

Experimental Data Snapshot

  • Resolution: 1.83 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 

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Structural Basis for the Activity of Drugs that Inhibit Phosphodiesterases.

Card, G.L.England, B.P.Suzuki, Y.Fong, D.Powell, B.Lee, B.Luu, C.Tabrizizad, M.Gillette, S.Ibrahim, P.N.Artis, D.R.Bollag, G.Milburn, M.V.Kim, S.-H.Schlessinger, J.Zhang, K.Y.J.

(2004) Structure 12: 2233-2247

  • DOI: https://doi.org/10.1016/j.str.2004.10.004
  • Primary Citation of Related Structures:  
    1XLX, 1XLZ, 1XM4, 1XM6, 1XMU, 1XMY, 1XN0, 1XOM, 1XON, 1XOQ, 1XOR, 1XOS, 1XOT, 1XOZ, 1XP0

  • PubMed Abstract: 

    Phosphodiesterases (PDEs) comprise a large family of enzymes that catalyze the hydrolysis of cAMP or cGMP and are implicated in various diseases. We describe the high-resolution crystal structures of the catalytic domains of PDE4B, PDE4D, and PDE5A with ten different inhibitors, including the drug candidates cilomilast and roflumilast, for respiratory diseases. These cocrystal structures reveal a common scheme of inhibitor binding to the PDEs: (i) a hydrophobic clamp formed by highly conserved hydrophobic residues that sandwich the inhibitor in the active site; (ii) hydrogen bonding to an invariant glutamine that controls the orientation of inhibitor binding. A scaffold can be readily identified for any given inhibitor based on the formation of these two types of conserved interactions. These structural insights will enable the design of isoform-selective inhibitors with improved binding affinity and should facilitate the discovery of more potent and selective PDE inhibitors for the treatment of a variety of diseases.

  • Organizational Affiliation

    Plexxikon, Inc., 91 Bolivar Drive, Berkeley, CA 94710, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4D
A, B
349Homo sapiensMutation(s): 0 
Gene Names: PDE4D
UniProt & NIH Common Fund Data Resources
Find proteins for Q08499 (Homo sapiens)
Explore Q08499 
Go to UniProtKB:  Q08499
GTEx:  ENSG00000113448 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08499
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ROF

Download Ideal Coordinates CCD File 
FA [auth B],
Q [auth A]
C17 H14 Cl2 F2 N2 O3
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
R [auth B]
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
E [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
C2 H6 O2
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
S [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
ROF BindingDB:  1XOQ IC50: min: 0.13, max: 680 (nM) from 15 assay(s)
PDBBind:  1XOQ IC50: 0.68 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.83 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.899α = 90
b = 60.116β = 90
c = 163.996γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
ELVESdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Advisory, Data collection, Database references, Derived calculations