5TRF Ligase Ligase Inhibitor date Oct 26, 2016
title Mdm2 In Complex With Sar405838
authors J.L.Meagher, J.A.Stuckey
compound source
Molecule: E3 Ubiquitin-Protein Ligase Mdm2
Chain: A, B, C, D, E
Fragment: Residues 10-118
Synonym: Double Minute 2 Protein,Hdm2,Oncoprotein Mdm2,P53- Protein Mdm2;
Ec: 6.3.2.-
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mdm2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 43 21 2
R_factor 0.185 R_Free 0.208
crystal
cell
length a length b length c angle alpha angle beta angle gamma
138.849 138.849 83.707 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand 7HC, GOL, SO4 enzyme Ligase E.C.6.3.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, E, B


Primary referenceSAR405838: an optimized inhibitor of MDM2-p53 interaction that induces complete and durable tumor regression., Wang S, Sun W, Zhao Y, McEachern D, Meaux I, Barriere C, Stuckey JA, Meagher JL, Bai L, Liu L, Hoffman-Luca CG, Lu J, Shangary S, Yu S, Bernard D, Aguilar A, Dos-Santos O, Besret L, Guerif S, Pannier P, Gorge-Bernat D, Debussche L, Cancer Res. 2014 Oct 15;74(20):5855-65. doi: 10.1158/0008-5472.CAN-14-0799. Epub , 2014 Aug 21. PMID:25145672
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (176 Kb) [Save to disk]
  • Biological Unit Coordinates (5trf.pdb1.gz) 37 Kb
  • Biological Unit Coordinates (5trf.pdb2.gz) 37 Kb
  • Biological Unit Coordinates (5trf.pdb3.gz) 36 Kb
  • Biological Unit Coordinates (5trf.pdb4.gz) 36 Kb
  • Biological Unit Coordinates (5trf.pdb5.gz) 36 Kb
  • Biological Unit Coordinates (5trf.pdb6.gz) 71 Kb
  • Biological Unit Coordinates (5trf.pdb7.gz) 69 Kb
  • Biological Unit Coordinates (5trf.pdb8.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 5TRF
  • CSU: Contacts of Structural Units for 5TRF
  • Structure Factors (1246 Kb)
  • Retrieve 5TRF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5TRF from S2C, [Save to disk]
  • Re-refined 5trf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5TRF 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 5TRF
  • 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: [5trf_E] [5trf_C] [5trf_A] [5trf] [5trf_B] [5trf_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5TRF
  • Community annotation for 5TRF at PDBWiki (http://pdbwiki.org)

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