4W9L pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-3,3-dimethylbutanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 15) date
authors Gadd, M.S., Galdeano, C., Molle, I.van., Ciulli, A.
compound source
symmetry
R_factor
R_Free 0.2430
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.20
ligand 3JJ, 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] (449 Kb) [Save to disk]
  • Biological Unit Coordinates (4w9l.pdb1.gz) 112 Kb
  • Biological Unit Coordinates (4w9l.pdb2.gz) 112 Kb
  • Biological Unit Coordinates (4w9l.pdb3.gz) 114 Kb
  • Biological Unit Coordinates (4w9l.pdb4.gz) 114 Kb
  • LPC: Ligand-Protein Contacts for 4W9L
  • CSU: Contacts of Structural Units for 4W9L
  • Structure Factors (1508 Kb)
  • Retrieve 4W9L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4W9L from S2C, [Save to disk]
  • Re-refined 4w9l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4W9L 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 4W9L
  • 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 4W9L, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4w9l_K] [4w9l_F] [4w9l_G] [4w9l_E] [4w9l] [4w9l_B] [4w9l_A] [4w9l_C] [4w9l_I] [4w9l_J] [4w9l_L] [4w9l_D] [4w9l_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4W9L: [Skp1] [UBQ ] by SMART
    • Other resources with information on 4W9L
  • Community annotation for 4W9L 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