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: 2.20 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/jm401840s
  • Primary Citation of Related Structures:  
    4NWK, 4NWL

  • 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 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.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HCV NS3 1a Protease
A, B
219hepatitis C virus genotype 1aMutation(s): 10 
UniProt
Find proteins for A8DG50 (hepatitis C virus genotype 1a)
Explore A8DG50 
Go to UniProtKB:  A8DG50
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8DG50
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2R9
Query on 2R9

Download Ideal Coordinates CCD File 
C [auth A],
E [auth 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
C35 H46 Cl N5 O9 S
XRWSZZJLZRKHHD-WVWIJVSJSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
2R9 BindingDB:  4NWL IC50: 1 (nM) from 1 assay(s)
EC50: min: 1.2, max: 4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.412α = 90
b = 67.761β = 108.46
c = 61.307γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
CNXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-26
    Type: Initial release
  • Version 1.1: 2015-11-25
    Changes: Non-polymer description
  • Version 1.2: 2017-08-09
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations