3I8V

Crystal structure of human PDE4a with 4-(3-butoxy-4-methoxyphenyl)methyl-2-imidazolidone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of human PDE4a with 4-(3-butoxy-4-methoxyphenyl)methyl-2-imidazolidone

Cheng, R.K.Y.Crawley, L.Barker, J.Wood, M.Felicetti, B.Whittaker, M.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-specific 3',5'-cyclic phosphodiesterase 4A
A, B
354Homo sapiensMutation(s): 0 
Gene Names: PDE4A (DPDE2)
EC: 3.1.4.53
Find proteins for P27815 (Homo sapiens)
Go to Gene View: PDE4A
Go to UniProtKB:  P27815
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0MO
Query on 0MO

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Download CCD File 
A, B
(4R)-4-(3-butoxy-4-methoxybenzyl)imidazolidin-2-one
4-(3-butoxy-4-methoxyphenyl)methyl-2-imidazolidone
C15 H22 N2 O3
PDMUULPVBYQBBK-GFCCVEGCSA-N
 Ligand Interaction
ZN
Query on ZN

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

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

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Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSS
Query on CSS
A, B
L-PEPTIDE LINKINGC3 H7 N O2 S2CYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0MOIC50: 4300 nM (100) BINDINGDB
0MOEC50: 3300 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.187 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 105.406α = 90.00
b = 105.406β = 90.00
c = 165.252γ = 90.00
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance