4JVB

Crystal structure of PDE6D in complex with the inhibitor rac-2

Structural Biology Knowledgebase: 4JVB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.188

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4JVB

Classification: Protein binding / inhibitor

Total Structure Weight: 18145.96

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

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1M0
Query on 1M0

B 1-benzyl-2-(4-{[(2R)-2-(2-phenyl-1H-benzimidazol- 1-yl)pent-4-en-1-yl]oxy}phenyl)-1H-benzimidazole
C38 H32 N4 O
VETKHSOXOHNPCG-WJOKGBTCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
1M0 N/A in BindingDB
Kd: 39 nM  BindingMOAD
Kd: 39 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.188
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 55.68 α = 90.00
b = 55.68 β = 90.00
c = 116.55 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