4NWK | pdb_00004nwk

Crystal structure of hepatis c virus protease (ns3) complexed with bms-605339 aka n-(tert-butoxycarbonyl)-3-me thyl-l-valyl-(4r)-n-((1r,2s)-1-((cyclopropylsulfonyl)carba moyl)-2-vinylcyclopropyl)-4-((6-methoxy-1-isoquinolinyl)ox y)-l-prolinamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 
    0.213 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4NWK

Ligand Structure Quality Assessment 


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: https://doi.org/10.1021/jm401840s
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 24.78 kDa 
  • Atom Count: 1,715 
  • Modeled Residue Count: 188 
  • Deposited Residue Count: 219 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HCV NS3 1a Protease219hepatitis 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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2R8

Query on 2R8



Download:Ideal Coordinates CCD File
B [auth A]N-(tert-butoxycarbonyl)-3-methyl-L-valyl-(4R)-N-{(1R,2S)-1-[(cyclopropylsulfonyl)carbamoyl]-2-ethenylcyclopropyl}-4-[(6-methoxyisoquinolin-1-yl)oxy]-L-prolinamide
C35 H47 N5 O9 S
IYWRCNFZPNEADN-CXODAYGWSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
2R8 BindingDB:  4NWK IC50: min: 2, max: 187 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free:  0.213 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.197α = 90
b = 103.852β = 90
c = 45.298γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
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: 2017-08-09
    Changes: Source and taxonomy
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations