4JV8

The crystal structure of PDE6D in complex with rac-S1

Structural Biology Knowledgebase: 4JV8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.180

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4JV8

Classification: Protein binding / inhibitor

Total Structure Weight: 18181.95

Macromolecule Entities
Molecule Chains Length Organism Details
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta B 152 Homo sapiens Gene Name(s): PDE6D Gene View PDED
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1M1
Query on 1M1

B (6R)-6-(pyridin-2-yl)-5,6-dihydrobenzimidazo[1,2- c]quinazoline
C19 H14 N4
ZMZZAQWHHFSQPH-LJQANCHMSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
1M1 N/A in BindingDB
N/A in BindingMoad
Kd: 1420 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.180
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 55.97 α = 90.00
b = 55.97 β = 90.00
c = 115.56 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-03-25
  • Released Date: 2013-05-22
  • Deposition author(s): Gunther, Z., Papke, B., Ismail, S., Vartak, N., Chandra, A., Hoffmann, M., Hahn, S., Triola, G., Wittinghofer, A., Bastiaens, P., Waldmann, H.

Revision History

  • 2013-06-05
    Type: Citation | Details: Citation update