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 

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Ligand Structure Quality Assessment 


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: https://doi.org/10.1016/j.bmcl.2010.08.022
  • Primary Citation of Related Structures:  
    2XNI

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NS3 PROTEASE
A, B
198Hepacivirus hominisMutation(s): 0 
UniProt
Find proteins for P27958 (Hepatitis C virus genotype 1a (isolate H77))
Explore P27958 
Go to UniProtKB:  P27958
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27958
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NS4A COFACTOR
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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TR8
Query on TR8

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

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

Download Ideal Coordinates CCD File 
G [auth A],
I [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
TR8 PDBBind:  2XNI IC50: 43 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment 


Entry History