2XNI

Protein-ligand complex of a novel macrocyclic HCV NS3 protease inhibitor derived from amino cyclic boronates


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Novel Macrocyclic Hcv Ns3 Protease Inhibitors Derived from Alpha-Amino Cyclic Boronates.

Li, X.Zhang, Y.Liu, Y.Ding, C.Z.Zhou, Y.Li, Q.Plattner, J.J.Baker, S.J.Zhang, S.Kazmierski, W.M.Wright, L.L.Smith, G.K.Grimes, R.M.Crosby, R.M.Creech, K.L.Carballo, L.H.Slater, M.J.Jarvest, R.L.Thommes, P.Hubbard, J.A.Convery, M.A.Nassau, P.M.Mcdowell, W.Skarzynski, T.J.Qian, X.Fan, D.Liao, L.Ni, Z.-J.Pennicott, L.E.Zou, W.Wright, J.

(2010) Bioorg Med Chem Lett 20: 5695

  • DOI: 10.1016/j.bmcl.2010.08.022
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A novel series of P2-P4 macrocyclic HCV NS3/4A protease inhibitors with α-amino cyclic boronates as warheads at the P1 site was designed and synthesized. When compared to their linear analogs, these macrocyclic inhibitors exhibited a remarkable impro ...

    A novel series of P2-P4 macrocyclic HCV NS3/4A protease inhibitors with α-amino cyclic boronates as warheads at the P1 site was designed and synthesized. When compared to their linear analogs, these macrocyclic inhibitors exhibited a remarkable improvement in cell-based replicon activities, with compounds 9a and 9e reaching sub-micromolar potency in replicon assay. The SAR around α-amino cyclic boronates clearly established the influence of ring size, chirality and of the substitution pattern. Furthermore, X-ray structure of the co-crystal of inhibitor 9a and NS3 protease revealed that Ser-139 in the enzyme active site traps boron in the warhead region of 9a, thus establishing its mode of action.


    Organizational Affiliation

    Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, CA 94303, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NS3 PROTEASE
A, B
198Hepacivirus CMutation(s): 0 
Find proteins for C1KHZ7 (Hepacivirus C)
Go to UniProtKB:  C1KHZ7

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NS4A COFACTOR
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
TR8
Query on TR8

Download CCD File 
A
(1-{[(10-tert-butyl-15,15-dimethyl-3,9,12-trioxo-6,7,9,10,11,12,14,15,16,17,18,19,23,23a-tetradecahydro-1H,5H-2,23:5,8-dimethano-4,13,2,8,11-benzodioxatriazacyclohenicosin-7(3H)-yl)carbonyl]amino}-3-hydroxypropyl)(trihydroxy)borate(1-)
C32 H52 B N4 O10
TWUMYENOHGWFCN-UHFFFAOYSA-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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TR8IC50:  43   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 233.289α = 90
b = 233.289β = 90
c = 78.067γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2012-09-26
    Changes: Database references