1MKD

crystal structure of PDE4D catalytic domain and zardaverine complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.245

Literature

Macromolecules
Sequence Display for 1MKD

Classification: HYDROLASE

Total Structure Weight: 457099.84

Macromolecule Entities
Molecule Chains Length Organism Details
Phosphodiesterase 4D A, B, C..., D, E, F, G, H, I, J, K, LA, B, C, D, E, F, G, H, I, J, K, L 328 Homo sapiens EC#: 3.1.4.53 IUBMB
Fragment: catalytic domain
Mutation: R439P
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
ZAR
Query on ZAR

A, B, C, D, E, F, G, H, I, J, K, L 6-(4-DIFLUOROMETHOXY-3-METHOXY-PHENYL)-2H- PYRIDAZIN-3-ONE
C12 H10 F2 N2 O3
HJMQDJPMQIHLPB-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C, D, E, F, G, H, I, J, K, L ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D, E, F, G, H, I, J, K, L MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ZAR IC50: 390 - 930 nM (87 - 99) BindingDB

N/A in BindingMoad
IC50: 160 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.245
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 97.32 α = 90.00
b = 164.57 β = 90.00
c = 325.54 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-08-29
  • Released Date: 2003-03-01
  • Deposition author(s): Lee, M.E., Markowitz, J., Lee, J.-O., Lee, H.

Revision History

  • Version 1_0: 2003-03-01

    Type: Initial release

  • Version 1_1: 2008-04-28

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance