4JV6

The crystal structure of PDE6D in complex to inhibitor-1

Structural Biology Knowledgebase: 4JV6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.175

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4JV6

Classification: Protein binding / inhibitor

Total Structure Weight: 18154.02

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
18F
Query on 18F

B 1-benzyl-2-phenyl-1H-benzimidazole
C20 H16 N2
LCFXRSKBJWQHON-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
18F N/A in BindingDB
Kd: 165 nM  BindingMOAD
Kd: 217 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.175
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 55.36 α = 90.00
b = 55.36 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