2XCN

Crystal structure of HCV NS3 protease with a boronate inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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
  • 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
NS3 PROTEASEA, B198Hepacivirus CMutation(s): 0 
UniProt
Find proteins for Q91RS4 (Hepacivirus C)
Explore Q91RS4 
Go to UniProtKB:  Q91RS4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91RS4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NS4AC, D23Hepacivirus CMutation(s): 0 
UniProt
Find proteins for C9WU77 (Hepacivirus C)
Explore C9WU77 
Go to UniProtKB:  C9WU77
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC9WU77
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C8D
Query on C8D

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
N-[(CYCLOPENTYLOXY)CARBONYL]-3-METHYL-L-VALYL-(4R)-N-{(1R)-3-HYDROXY-1-[HYDROXY(OXIDO)BORANYL]PROPYL}-4-(ISOQUINOLIN-1-YLOXY)-L-PROLINAMIDE
C29 H40 B N4 O8
COHYIEQRPXQCHT-AYVPJYCDSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
J [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
C8D PDBBind:  2XCN IC50: 120 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 231.37α = 90
b = 231.37β = 90
c = 75.667γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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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