1RTL

CRYSTAL STRUCTURE OF HCV NS3 PROTEASE DOMAIN: NS4A PEPTIDE COMPLEX WITH COVALENTLY BOUND PYRROLIDINE-5,5-TRANSLACTAM INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Pyrrolidine-5,5-trans-lactams. 4. Incorporation of a P3/P4 urea leads to potent intracellular inhibitors of hepatitis C virus NS3/4A protease

Slater, M.J.Amphlett, E.M.Andrews, D.M.Bamborough, P.Carey, S.J.Johnson, M.R.Jones, P.S.Mills, G.Parry, N.R.Somers, D.O.Stewart, A.J.Skarzynski, T.

(2003) Org Lett 5: 4627-4630

  • DOI: 10.1021/ol035826v
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • [reaction: see text] In this, the first of two Letters, we describe how a P3/P4 urea linking unit was used to greatly enhance the biochemical and replicon potency of inhibitors based upon the pyrrolidine-5,5-trans-lactam template. Compound 7b demonst ...

    [reaction: see text] In this, the first of two Letters, we describe how a P3/P4 urea linking unit was used to greatly enhance the biochemical and replicon potency of inhibitors based upon the pyrrolidine-5,5-trans-lactam template. Compound 7b demonstrated a 100 nM IC(50) in the replicon cell-based surrogate HCV assay.


    Related Citations: 
    • Pyrrolidine-5,5-Trans-Lactams. 2. The Use of X-Ray Crystal Structure Data in the Optimisation of P3 and P4 Substituents
      Andrews, D.M., Chaignot, H., Coomber, B.A., Good, A.C., Hind, S.L., Johnson, M.R., Jones, P.S., Mills, G., Robinson, J.E., Skarzynski, T., Slater, M.J., Somers, D.O.
      (2002) Org Lett 4: 4479

    Organizational Affiliation

    GlaxoSmithKline Medicines Research Center, Gunnels Wood Road, Stevenage, SG1 2NY, UK. martin.j.slater@gsk.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NS3 protease/helicase
A, B
200Hepacivirus CMutation(s): 1 
Gene Names: H STRAIN
EC: 3.4.22 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P26664 (Hepatitis C virus genotype 1a (isolate 1))
Go to UniProtKB:  P26664
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NS4A COFACTOR
C, D
23N/AMutation(s): 0 
Find proteins for O39914 (Hepacivirus C)
Go to UniProtKB:  O39914
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CPX
Query on CPX

Download CCD File 
A
N-[(2R,3S)-1-((2S)-2-{[(CYCLOPENTYLAMINO)CARBONYL]AMINO}-3-METHYLBUTANOYL)-2-(1-FORMYL-1-CYCLOBUTYL)PYRROLIDINYL]CYCLOPROPANECARBOXAMIDE
C24 H38 N4 O4
GCDRFILPPBOJLM-UFYCRDLUSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CPXIC50 :  2600   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 224.082α = 90
b = 224.082β = 90
c = 75.694γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance