1XOT

Catalytic Domain Of Human Phosphodiesterase 4B In Complex With Vardenafil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.str.2004.10.004
  • Primary Citation of Related Structures:  

  • 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 w ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-specific 3',5'-cyclic phosphodiesterase 4B
B, A
398Homo sapiensMutation(s): 0 
Gene Names: PDE4B (DPDE4)
EC: 3.1.4.53
Find proteins for Q07343 (Homo sapiens)
Go to Gene View: PDE4B
Go to UniProtKB:  Q07343
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
VDN
Query on VDN

Download SDF File 
Download CCD File 
A, B
2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-5-METHYL-7-PROPYLIMIDAZO[5,1-F][1,2,4]TRIAZIN-4(1H)-ONE
VARDENAFIL, LEVITRA
C23 H32 N6 O4 S
SECKRCOLJRRGGV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A, B
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VDNIC50: 3800 nM (100) BINDINGDB
VDNIC50: 3800 nM BINDINGMOAD
VDNIC50: 3800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 89.841α = 90.00
b = 94.423β = 90.00
c = 108.755γ = 90.00
Software Package:
Software NamePurpose
EPMRphasing
Blu-Icedata collection
ELVESdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance