Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 168.74 kDa 
• Atom Count: 11207 
• Residue Count: 1322 
• Unique protein chains: 1

2FM5

Crystal structure of PDE4D2 in complex with inhibitor L-869299

• DOI: 10.2210/pdb2FM5/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-01-07 Released: 2006-03-28 
• Deposition Author(s): Huai, Q., Sun, Y., Wang, H., Macdonald, D., Aspiotis, R., Robinson, H., Huang, Z., Ke, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.260 
• R-Value Work: 0.231 
• R-Value Observed: 0.231 

Literature

Enantiomer Discrimination Illustrated by the High Resolution Crystal Structures of Type 4 Phosphodiesterase

Huai, Q., Sun, Y., Wang, H., Macdonald, D., Aspiotis, R., Robinson, H., Huang, Z., Ke, H.

(2006) J Med Chem 49: 1867-1873

• PubMed: 16539372 
• DOI: 10.1021/jm051273d
• Primary Citation of Related Structures:  
  2FM0, 2FM5


• PubMed Abstract: 
  

Type 4 phosphodiesterase (PDE4) inhibitors are emerging as new treatments for a number of disorders including asthma and chronic obstructive pulmonary disease. Here we report the biochemical characterization on the second generation inhibitor (+)-1 (L-, IC50=0.4 nM) and its enantiomer (-)-1 (L-, IC50=43 nM) and their cocrystal structures with PDE4D at 2.0 A resolution. Despite the 107-fold affinity difference, both enantiomers interact with the same sets of residues in the rigid active site. The weaker (-)-1 adopts an unfavorable conformation to preserve the pivotal interactions between the Mg-bound waters and the N-oxide of pyridine. These structures support a model in which inhibitors are anchored by the invariant glutamine at one end and the metal-pocket residues at another end. This model provides explanations for most of the observed structure-activity relationship and the metal ion dependency of the catechol-ether based inhibitors and should facilitate their further design.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, North Carolina 27599-7260, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-specific 3',5'-cyclic phosphodiesterase 4D	A, B, C, D	361	Homo sapiens	Mutation(s): 0  Gene Names: PDE4D2, PDE4D, DPDE3 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 GTEx  ENSG00000113448

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M99	A, B, C, D	(R)-3-(2-(3-CYCLOPROPOXY-4-(DIFLUOROMETHOXY)PHENYL)-2-(5-(1,1,1,3,3,3-HEXAFLUORO-2-HYDROXYPROPAN-2-YL)THIAZOL-2-YL)ETHYL)PYRIDINE 1-OXIDE C23 H18 F8 N2 O4 S SPOLCPORTSDTGD-OAHLLOKOSA-N
ZN	A, B, C, D	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	A, B, C, D	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
M99	IC50:  40   nM  BindingDB
M99	IC50:  43   nM  Binding MOAD
M99	IC50 :  43   nM  PDBBind
M99	IC50:  43   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.260 
• R-Value Work: 0.231 
• R-Value Observed: 0.231 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.357	α = 90
b = 112.812	β = 90
c = 161.079	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-01-07 
• Released Date: 2006-03-28 
Deposition Author(s): Huai, Q., Sun, Y., Wang, H., Macdonald, D., Aspiotis, R., Robinson, H., Huang, Z., Ke, H.

Revision History 

• Version 1.0: 2006-03-28
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance