6MVQ

HCV NS5B 1b N316 bound to Compound 31


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Design of N-Benzoxaborole Benzofuran GSK8175-Optimization of Human Pharmacokinetics Inspired by Metabolites of a Failed Clinical HCV Inhibitor.

Chong, P.Y.Shotwell, J.B.Miller, J.Price, D.J.Maynard, A.Voitenleitner, C.Mathis, A.Williams, S.Pouliot, J.J.Creech, K.Wang, F.Fang, J.Zhang, H.Tai, V.W.Turner, E.Kahler, K.M.Crosby, R.Peat, A.J.

(2019) J Med Chem 62: 3254-3267

  • DOI: 10.1021/acs.jmedchem.8b01719
  • Primary Citation of Related Structures:  
    6MVK, 6MVO, 6MVP, 6MVQ

  • PubMed Abstract: 
  • We previously described the discovery of GSK5852 (1), a non-nucleoside polymerase (NS5B) inhibitor of hepatitis C virus (HCV), in which an N-benzyl boronic acid was essential for potent antiviral activity. Unfortunately, facile benzylic oxidation resulted in a short plasma half-life (5 h) in human volunteers, and a backup program was initiated to remove metabolic liabilities associated with 1 ...

    We previously described the discovery of GSK5852 (1), a non-nucleoside polymerase (NS5B) inhibitor of hepatitis C virus (HCV), in which an N-benzyl boronic acid was essential for potent antiviral activity. Unfortunately, facile benzylic oxidation resulted in a short plasma half-life (5 h) in human volunteers, and a backup program was initiated to remove metabolic liabilities associated with 1. Herein, we describe second-generation NS5B inhibitors including GSK8175 (49), a sulfonamide- N-benzoxaborole analog with low in vivo clearance across preclinical species and broad-spectrum activity against HCV replicons. An X-ray structure of NS5B protein cocrystallized with 49 revealed unique protein-inhibitor interactions mediated by an extensive network of ordered water molecules and the first evidence of boronate complex formation within the binding pocket. In clinical studies, 49 displayed a 60-63 h half-life and a robust decrease in viral RNA levels in HCV-infected patients, thereby validating our hypothesis that reducing benzylic oxidation would improve human pharmacokinetics and lower efficacious doses relative to 1.


    Related Citations: 
    • Discovery of a potent boronic acid derived inhibitor of the HCV RNA-dependent RNA polymerase.
      Maynard, A., Crosby, R.M., Ellis, B., Hamatake, R., Hong, Z., Johns, B.A., Kahler, K.M., Koble, C., Leivers, A., Leivers, M.R., Mathis, A., Peat, A.J., Pouliot, J.J., Roberts, C.D., Samano, V., Schmidt, R.M., Smith, G.K., Spaltenstein, A., Stewart, E.L., Thommes, P., Turner, E.M., Voitenleitner, C., Walker, J.T., Waitt, G., Weatherhead, J., Weaver, K., Williams, S., Wright, L., Xiong, Z.Z., Haigh, D., Shotwell, J.B.
      (2014) J Med Chem 57: 1902

    Organizational Affiliation

    GlaxoSmithKline , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HCV PolymeraseA, B563Hepatitis C virus subtype 1bMutation(s): 2 
EC: 2.7.7.48 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
UniProt
Find proteins for Q99AU2 (Hepatitis C virus subtype 1b)
Explore Q99AU2 
Go to UniProtKB:  Q99AU2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99AU2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K4M
Query on K4M

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(4-{1-[5-cyclopropyl-2-(4-fluorophenyl)-3-(methylcarbamoyl)-1-benzofuran-6-yl]-1H-1,2,4-triazol-5-yl}-2-fluorophenyl)boronic acid
C27 H21 B F2 N4 O4
JILXKKKBOFQHHM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.811α = 90
b = 106.565β = 90
c = 126.509γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release