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


Ligand Structure Quality Assessment 


This is version 1.3 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
  • Primary Citation of Related Structures:  
    1RTL

  • 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 demonstrated a 100 nM IC(50) in the replicon cell-based surrogate HCV assay ...

    [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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NS3 protease/helicaseA, B200Hepacivirus 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)
UniProt
Find proteins for P26664 (Hepatitis C virus genotype 1a (isolate 1))
Explore P26664 
Go to UniProtKB:  P26664
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NS4A COFACTORC, D23N/AMutation(s): 0 
UniProt
Find proteins for O39914 (Hepacivirus C)
Explore O39914 
Go to UniProtKB:  O39914
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CPX (Subject of Investigation/LOI)
Query on CPX

Download Ideal Coordinates CCD File 
F [auth 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 Ideal Coordinates CCD File 
E [auth A], G [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
CPX PDBBind:  1RTL IC50: 2600 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations