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


Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1016/j.bmcl.2010.04.129
  • Primary Citation of Related Structures:  
    2XCF, 2XCN

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NS3 PROTEASE
A, B
198Hepacivirus hominisMutation(s): 1 
UniProt
Find proteins for C1KHN2 (Hepacivirus hominis)
Explore C1KHN2 
Go to UniProtKB:  C1KHN2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1KHN2
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NS4A
C, D
23Hepacivirus hominisMutation(s): 0 
UniProt
Find proteins for C9WU77 (Hepacivirus hominis)
Explore C9WU77 
Go to UniProtKB:  C9WU77
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC9WU77
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BBQ
Query on BBQ

Download Ideal Coordinates CCD File 
G [auth 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
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
I [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.5: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other