2XCF

Crystal structure of HCV NS3 protease with a boronate inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Synthesis and Evaluation of Novel Alpha-Amino Cyclic Boronates as Inhibitors of Hcv Ns3 Protease.

Li, X.Zhang, Y.-K.Liu, Y.Ding, C.Z.Li, Q.Zhou, Y.Plattner, J.J.Baker, S.J.Qian, X.Fan, D.Liao, L.Ni, Z.-J.White, G.V.Mordaunt, J.E.Lazarides, L.X.Slater, M.J.Jarvest, R.L.Edge, C.M.Hubbard, J.A.Nassau, P.Mcdowell, B.Skarzynski, T.J.Thommes, P.Ellis, M.Rowland, P.Somers, D.O.Kazmierski, W.M.Grimes, R.M.Wright, L.L.Smith, G.K.Zou, W.Wright, J.Pennicott, L.E.

(2010) Bioorg Med Chem Lett 20: 3550

  • DOI: 10.1016/j.bmcl.2010.04.129
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • We have designed and synthesized a novel series of alpha-amino cyclic boronates and incorporated them successfully in several acyclic templates at the P1 position. These compounds are inhibitors of the HCV NS3 serine protease, and structural studies ...

    We have designed and synthesized a novel series of alpha-amino cyclic boronates and incorporated them successfully in several acyclic templates at the P1 position. These compounds are inhibitors of the HCV NS3 serine protease, and structural studies show that they inhibit the NS3 protease by trapping the Ser-139 hydroxyl group in the active site. Synthetic methodologies and SARs of this series of compounds are described.


    Organizational Affiliation

    Anacor Pharmaceuticals, Inc., Palo Alto, CA 94303, USA. xli@anacor.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NS3 PROTEASE
A, B
198Hepacivirus CMutation(s): 1 
Find proteins for C1KHN2 (Hepacivirus C)
Go to UniProtKB:  C1KHN2

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NS4A
C, D
23Hepacivirus CMutation(s): 0 
Find proteins for C9WU77 (Hepacivirus C)
Go to UniProtKB:  C9WU77
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BBQ
Query on BBQ

Download CCD File 
A
CYCLOPENTYL N-[(2S)-1-[(2S,4R)-2-[[(4R)-8-HYDROXY-1,6,10-TRIOXA-5$L^{4}-BORASPIRO[4.5]DECAN-4-YL]CARBAMOYL]-4-ISOQUINOLIN-1-YLOXY-PYRROLIDIN-1-YL]-3,3-DIMETHYL-1-OXO-BUTAN-2-YL]CARBAMATE
C32 H44 B N4 O9
MSXWUFQOFQGEEP-GYUKIKGESA-N
 Ligand Interaction
ZN
Query on ZN

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

Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 225.889α = 90
b = 225.889β = 90
c = 75.196γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2010-06-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-01-30
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2019-02-06
    Changes: Data collection, Experimental preparation