4JVF

The Crystal structure of PDE6D in complex with the inhibitor (s)-5

Structural Biology Knowledgebase: 4JVF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.207

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4JVF

Classification: Protein binding / inhibitor

Total Structure Weight: 18224.11

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
17X
Query on 17X

B (2S)-2-(2-phenyl-1H-benzimidazol-1-yl)-2- (piperidin-4-yl)ethyl 1-(1-benzyl-1H-benzimidazol- 2-yl)piperidine-4-carboxylate
C40 H42 N6 O2
WDALFJYWTFDSRP-DIPNUNPCSA-N
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
17X N/A in BindingDB
Kd: 10 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.207
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 55.91 α = 90.00
b = 55.91 β = 90.00
c = 116.67 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