5VFC Transcription Inhibitor date Apr 07, 2017
title Wdr5 Bound To Inhibitor Mm-589
authors J.A.Stuckey
compound source
Molecule: Wd Repeat-Containing Protein 5
Chain: A
Synonym: Bmp2-Induced 3-Kb Gene Protein
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Wdr5, Big3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.148 R_Free 0.174
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.348 58.559 56.801 90.00 96.16 90.00
method X-Ray Diffractionresolution 1.64 Å
ligand 9BA, EDO, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceDiscovery of a Highly Potent, Cell-Permeable Macrocyclic Peptidomimetic (MM-589) Targeting the WD Repeat Domain 5 Protein (WDR5)-Mixed Lineage Leukemia (MLL) Protein-Protein Interaction., Karatas H, Li Y, Liu L, Ji J, Lee S, Chen Y, Yang J, Huang L, Bernard D, Xu J, Townsend EC, Cao F, Ran X, Li X, Wen B, Sun D, Stuckey JA, Lei M, Dou Y, Wang S, J Med Chem. 2017 Jun 22;60(12):4818-4839. doi: 10.1021/acs.jmedchem.6b01796. Epub, 2017 Jun 12. PMID:28603984
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (104 Kb) [Save to disk]
  • Biological Unit Coordinates (5vfc.pdb1.gz) 99 Kb
  • LPC: Ligand-Protein Contacts for 5VFC
  • CSU: Contacts of Structural Units for 5VFC
  • Structure Factors (1218 Kb)
  • Retrieve 5VFC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VFC from S2C, [Save to disk]
  • Re-refined 5vfc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5VFC 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 5VFC
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vfc_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5VFC
  • Community annotation for 5VFC at PDBWiki (http://pdbwiki.org)

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