Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 167203.73 
• Atom Count: 10870 
• Residue Count: 1440 
• Unique protein chains: 1

1OYN

Crystal structure of PDE4D2 in complex with (R,S)-rolipram

• DOI: 10.2210/pdb1OYN/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2003-04-05 Released: 2003-07-15 
• Deposition Author(s): Huai, Q., Wang, H., Sun, Y., Kim, H.Y., Liu, Y., Ke, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.266 

Literature

Three-dimensional structures of PDE4D in complex with roliprams and implication on inhibitor selectivity

Huai, Q., Wang, H., Sun, Y., Kim, H.Y., Liu, Y., Ke, H.

(2003) Structure 11: 865-873

• PubMed: 12842049 
• Primary Citation of Related Structures:  
  1Q9M


• PubMed Abstract: 
  

Selective inhibitors against the 11 families of cyclic nucleotide phosphodiesterases (PDEs) are used to treat various human diseases. How the inhibitors selectively bind the conserved PDE catalytic domains is unknown. The crystal structures of the PDE4D2 catalytic domain in complex with (R)- or (R,S)-rolipram suggest that inhibitor selectivity is determined by the chemical nature of amino acids and subtle conformational changes of the binding pockets. The conformational states of Gln369 in PDE4D2 may play a key role in inhibitor recognition. The corresponding Y329S mutation in PDE7 may lead to loss of the hydrogen bonds between rolipram and Gln369 and is thus a possible reason explaining PDE7's insensitivity to rolipram inhibition. Docking of the PDE5 inhibitor sildenafil into the PDE4 catalytic pocket further helps understand inhibitor selectivity.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
cAMP-specific phosphodiesterase PDE4D2	A, B, C, D	360	Homo sapiens	Mutation(s): 0  Gene Names: PDE4D (DPDE3) EC: 3.1.4.53
Find proteins for Q08499 (Homo sapiens) Go to Gene View: PDE4D Go to UniProtKB:  Q08499

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, B, C, D	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ROL	A, B, C, D	ROLIPRAM (4R)-[3-(CYCLOPENTYLOXY)-4-METHOXYPHENYL]-2-PYRROLIDINONE C16 H21 N O3 HJORMJIFDVBMOB-LBPRGKRZSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
4RR	EC50: 1100 nM (100) BINDINGDB
4RR	IC50: 20 - 17000 nM (100) BINDINGDB
4RR	Ki: 1.6 - 8460 nM (100) BINDINGDB
ROL	IC50: 550 nM BINDINGMOAD
ROL	IC50: 550 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.266 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 99.785	α = 90.00
b = 111.529	β = 90.00
c = 160.025	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-04-05 
• Released Date: 2003-07-15 
• Deposition Author(s): Huai, Q., Wang, H., Sun, Y., Kim, H.Y., Liu, Y., Ke, H.

Revision History 

• Version 1.0: 2003-07-15
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance