4W9K pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-3-phenylpropanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 14) date
authors Gadd, M.S., Galdeano, C., Molle, I.van., Ciulli, A.
compound source
symmetry
R_factor
R_Free 0.2596
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.10
ligand 3JO, CAS enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, J, D, G


H, K, E, B


Primary referenceStructure-Guided Design and Optimization of Small Molecules Targeting the Protein-Protein Interaction between the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor (HIF) Alpha Subunit with In Vitro Nanomolar Affinities., Galdeano C, Gadd MS, Soares P, Scaffidi S, Van Molle I, Birced I, Hewitt S, Dias DM, Ciulli A, J Med Chem. 2014 Aug 28. PMID:25166285
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (452 Kb) [Save to disk]
  • Biological Unit Coordinates (4w9k.pdb1.gz) 114 Kb
  • Biological Unit Coordinates (4w9k.pdb2.gz) 113 Kb
  • Biological Unit Coordinates (4w9k.pdb3.gz) 114 Kb
  • Biological Unit Coordinates (4w9k.pdb4.gz) 114 Kb
  • LPC: Ligand-Protein Contacts for 4W9K
  • CSU: Contacts of Structural Units for 4W9K
  • Structure Factors (1719 Kb)
  • Retrieve 4W9K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4W9K from S2C, [Save to disk]
  • Re-refined 4w9k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4W9K in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 4W9K
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4W9K, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4w9k_H] [4w9k_L] [4w9k_J] [4w9k_K] [4w9k_A] [4w9k_I] [4w9k_G] [4w9k] [4w9k_B] [4w9k_F] [4w9k_E] [4w9k_D] [4w9k_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4W9K: [Skp1] [UBQ ] by SMART
    • Other resources with information on 4W9K
  • Community annotation for 4W9K at PDBWiki (http://pdbwiki.org)

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science