2OBO Structure of HEPATITIS C VIRAL NS3 protease domain complexed with NS4A peptide and ketoamide SCH476776 date
authors Prongay, A.J., Guo, Z., Yao, N., Fischmann, T., Strickland, C., Myers, J., Weber, P.C., Malcolm, B., Beyer, B.M., Ingram, R., Pichardo, J., Hong, Z., Prosise, W.W., Ramanathan, L., Taremi, S.S., Yarosh-Tomaine, T., Zhang, R., Senior, M., Yang, R., Arasappan, A., Bennett, F., Bogen, S.F., Chen, K., Jao, E., Liu, Y., Love, R.G., Saksena, A.K., Venkatraman, S., Girijavallabhan, V., Njoroge, F.G., Madison, V.
compound source
symmetry
R_factor
R_Free 0.295
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.60
ligand BME, HUD, ZN BindingDB enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceDiscovery of the HCV NS3/4A protease inhibitor (1R,5S)-N-[3-amino-1-(cyclobutylmethyl)-2,3-dioxopropyl]-3- [2(S)-[[[(1,1-dimethylethyl)amino]carbonyl]amino]-3,3-dimethyl-1-oxobutyl] - 6,6-dimethyl-3-azabicyclo[3.1.0]hexan-2(S)-carboxamide (Sch 503034) II. Key steps in structure-based optimization., Prongay AJ, Guo Z, Yao N, Pichardo J, Fischmann T, Strickland C, Myers J Jr, Weber PC, Beyer BM, Ingram R, Hong Z, Prosise WW, Ramanathan L, Taremi SS, Yarosh-Tomaine T, Zhang R, Senior M, Yang RS, Malcolm B, Arasappan A, Bennett F, Bogen SL, Chen K, Jao E, Liu YT, Lovey RG, Saksena AK, Venkatraman S, Girijavallabhan V, Njoroge FG, Madison V, J Med Chem. 2007 May 17;50(10):2310-8. Epub 2007 Apr 20. PMID:17444623
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (68 Kb) [Save to disk]
  • Biological Unit Coordinates (2obo.pdb1.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 2OBO
  • CSU: Contacts of Structural Units for 2OBO
  • Likely Quarternary Molecular Structure file(s) for 2OBO
  • Structure Factors (1053 Kb)
  • Retrieve 2OBO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2OBO from S2C, [Save to disk]
  • Re-refined 2obo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2OBO 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 2OBO
  • 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 2OBO, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2obo] [2obo_D] [2obo_A] [2obo_C] [2obo_B]
  • SWISS-PROT database: [P27958] [Q9ELS8] [Q9QP06]
  • Domain organization of [POLG_HCVH] [Q9ELS8_9HEPC] [Q9QP06_9HEPC] by SWISSPFAM
    • Other resources with information on 2OBO
  • Community annotation for 2OBO at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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