4NWL

Crystal structure of hepatis c virus protease (ns3) complexed with bms-650032 aka n-(tert-butoxycarbonyl)-3-me thyl-l-valyl-(4r)-4-((7-chloro-4-methoxy-1-isoquinolinyl)o xy)-n-((1r,2s)-1-((cyclopropylsulfonyl)carbamoyl)-2-vinylc yclopropyl)-l-prolinamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery and Early Clinical Evaluation of BMS-605339, a Potent and Orally Efficacious Tripeptidic Acylsulfonamide NS3 Protease Inhibitor for the Treatment of Hepatitis C Virus Infection.

Scola, P.M.Wang, A.X.Good, A.C.Sun, L.Q.Combrink, K.D.Campbell, J.A.Chen, J.Tu, Y.Sin, N.Venables, B.L.Sit, S.Y.Chen, Y.Cocuzza, A.Bilder, D.M.D'Andrea, S.Zheng, B.Hewawasam, P.Ding, M.Thuring, J.Li, J.Hernandez, D.Yu, F.Falk, P.Zhai, G.Sheaffer, A.K.Chen, C.Lee, M.S.Barry, D.Knipe, J.O.Li, W.Han, Y.H.Jenkins, S.Gesenberg, C.Gao, Q.Sinz, M.W.Santone, K.S.Zvyaga, T.Rajamani, R.Klei, H.E.Colonno, R.J.Grasela, D.M.Hughes, E.Chien, C.Adams, S.Levesque, P.C.Li, D.Zhu, J.Meanwell, N.A.McPhee, F.

(2014) J.Med.Chem. 57: 1708-1729

  • DOI: 10.1021/jm401840s
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The discovery of BMS-605339 (35), a tripeptidic inhibitor of the NS3/4A enzyme, is described. This compound incorporates a cyclopropylacylsulfonamide moiety that was designed to improve the potency of carboxylic acid prototypes through the introducti ...

    The discovery of BMS-605339 (35), a tripeptidic inhibitor of the NS3/4A enzyme, is described. This compound incorporates a cyclopropylacylsulfonamide moiety that was designed to improve the potency of carboxylic acid prototypes through the introduction of favorable nonbonding interactions within the S1' site of the protease. The identification of 35 was enabled through the optimization and balance of critical properties including potency and pharmacokinetics (PK). This was achieved through modulation of the P2* subsite of the inhibitor which identified the isoquinoline ring system as a key template for improving PK properties with further optimization achieved through functionalization. A methoxy moiety at the C6 position of this isoquinoline ring system proved to be optimal with respect to potency and PK, thus providing the clinical compound 35 which demonstrated antiviral activity in HCV-infected patients.


    Related Citations: 
    • Image annotation and database mining to create a novel screen for the chemotype-dependent crystallization of HCV NS3 protease
      Klei, H.E.,Kish, K.,Russo, M.F.,Michalczyk, S.J.,Cahn, M.H.,Tredup, J.,Chang, C.,Khan, J.,Baldwin, E.T.
      (2011) CRYST.GROWTH DES. 11: 1143


    Organizational Affiliation

    Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development , 5 Research Parkway, Wallingford, Connecticut 06492, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HCV NS3 1a Protease
A, B
219Hepatitis C virus subtype 1aMutation(s): 10 
Find proteins for A8DG50 (Hepatitis C virus subtype 1a)
Go to UniProtKB:  A8DG50
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
2R9
Query on 2R9

Download SDF File 
Download CCD File 
A, B
N-(tert-butoxycarbonyl)-3-methyl-L-valyl-(4R)-4-[(7-chloro-4-methoxyisoquinolin-1-yl)oxy]-N-{(1R,2S)-1-[(cyclopropylsulfonyl)carbamoyl]-2-ethenylcyclopropyl}-L-prolinamide
Asunaprevir
C35 H46 Cl N5 O9 S
XRWSZZJLZRKHHD-WVWIJVSJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.246 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.412α = 90.00
b = 67.761β = 108.46
c = 61.307γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNXrefinement
PDB_EXTRACTdata extraction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-26
    Type: Initial release
  • Version 1.1: 2015-11-25
    Type: Non-polymer description
  • Version 1.2: 2017-08-09
    Type: Refinement description, Source and taxonomy