1ZKN

Structure of PDE4D2-IBMX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.226

Literature

Macromolecules
Sequence Display for 1ZKN

Classification: HYDROLASE

Total Structure Weight: 155274.73

Macromolecule Entities
Molecule Chains Length Organism Details
cAMP-specific 3',5'-cyclic phosphodiesterase 4D A, B, C, D 334 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 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
IBM
Query on IBM

A, B, C, D 3-ISOBUTYL-1-METHYLXANTHINE
C10 H14 N4 O2
APIXJSLKIYYUKG-UHFFFAOYSA-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)
MG
Query on MG

A, B, C, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
IBM N/A in BindingDB
N/A in BindingMoad
IC50: 31000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.226
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 99.70 α = 90.00
b = 111.70 β = 90.00
c = 159.39 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-05-03
  • Released Date: 2005-05-17
  • Deposition author(s): Huai, Q., Liu, Y., Francis, S.H., Corbin, J.D., Ke, H.
  • Previous versions: 1RKO

Revision History

  • 2008-04-30
    Type: Version format compliance
  • 2011-07-13
    Type: Version format compliance