Crystal structure of HCV NS3/4A protease A156T variant in complex with 5172-Linear (MK-5172 linear analogue)

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.205 

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Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Structural and Thermodynamic Effects of Macrocyclization in HCV NS3/4A Inhibitor MK-5172.

Soumana, D.I.Kurt Yilmaz, N.Prachanronarong, K.L.Aydin, C.Ali, A.Schiffer, C.A.

(2016) ACS Chem Biol 11: 900-909

  • DOI: https://doi.org/10.1021/acschembio.5b00647
  • Primary Citation of Related Structures:  
    5EPN, 5EPY, 5EQQ, 5ETX

  • PubMed Abstract: 

    Recent advances in direct-acting antivirals against Hepatitis C Virus (HCV) have led to the development of potent inhibitors, including MK-5172, that target the viral NS3/4A protease with relatively low susceptibility to resistance. MK-5172 has a P2-P4 macrocycle and a unique binding mode among current protease inhibitors where the P2 quinoxaline packs against the catalytic residues H57 and D81. However, the effect of macrocyclization on this binding mode is not clear, as is the relation between macrocyclization, thermodynamic stabilization, and susceptibility to the resistance mutation A156T. We have determined high-resolution crystal structures of linear and P1-P3 macrocyclic analogs of MK-5172 bound to WT and A156T protease and compared these structures, their molecular dynamics, and experimental binding thermodynamics to the parent compound. We find that the "unique" binding mode of MK-5172 is conserved even when the P2-P4 macrocycle is removed or replaced with a P1-P3 macrocycle. While beneficial to decreasing the entropic penalty associated with binding, the constraint exerted by the P2-P4 macrocycle prevents efficient rearrangement to accommodate the A156T mutation, a deficit alleviated in the linear and P1-P3 analogs. Design of macrocyclic inhibitors against NS3/4A needs to achieve the best balance between exerting optimal conformational constraint for enhancing potency, fitting within the substrate envelope and allowing adaptability to be robust against resistance mutations.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , 364 Plantation Street, Worcester, Massachusetts 01605, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NS3 protease
A, B, C, D
194Hepacivirus hominisMutation(s): 2 
Find proteins for C1KIK8 (Hepacivirus hominis)
Explore C1KIK8 
Go to UniProtKB:  C1KIK8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1KIK8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 5RS

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
K [auth C],
M [auth D]
~{tert}-butyl ~{N}-[(2~{S})-1-[(2~{S},4~{R})-2-[[(1~{R},2~{R})-1-(cyclopropylsulfonylcarbamoyl)-2-ethyl-cyclopropyl]carbamoyl]-4-(3-ethyl-7-methoxy-quinoxalin-2-yl)oxy-pyrrolidin-1-yl]-3,3-dimethyl-1-oxidanylidene-butan-2-yl]carbamate
C36 H52 N6 O9 S
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
J [auth C],
L [auth D]
Query on CL

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.441α = 90
b = 63.232β = 91.65
c = 92.304γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01-AI085051
Michigan Economic Development Corporation and the Michigan Technology Tri-CorridoUnited States085P1000817

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-04-27
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Advisory, Author supporting evidence, Derived calculations
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Advisory, Data collection, Database references, Refinement description