1OYN

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

Structural Biology Knowledgebase: 1OYN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Observed: 0.233

Literature

Macromolecules
Sequence Display for 1OYN

Classification: HYDROLASE

Total Structure Weight: 167205.08

Macromolecule Entities
Molecule Chains Length Organism Details
cAMP-specific phosphodiesterase PDE4D2 A, B, C, D 360 Homo sapiens EC#: 3.1.4.53 IUBMB
Fragment: catalytic domain
Gene Name(s): PDE4D Gene View DPDE3
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ROL
Query on ROL

A, B, C, D ROLIPRAM
(4R)-[3-(CYCLOPENTYLOXY)-4-METHOXYPHENYL]- 2-PYRROLIDINONE (Synonym)
C16 H21 N O3
HJORMJIFDVBMOB-LBPRGKRZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C, D ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ROL EC50: 220 - 1100 nM (85 - 100) BindingDB
IC50: 20 - 17000 nM (85 - 100) BindingDB
Ki: 3.8 - 8460 nM (85 - 100) BindingDB

IC50: 550 nM  BindingMOAD
IC50: 550 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Observed: 0.233
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 99.79 α = 90.00
b = 111.53 β = 90.00
c = 160.02 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



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

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4