7TCZ

Human cytomegalovirus protease mutant (C84A, C87A, C138A, C202A) in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Inhibiting a dynamic viral protease by targeting a non-catalytic cysteine.

Hulce, K.R.Jaishankar, P.Lee, G.M.Bohn, M.F.Connelly, E.J.Wucherer, K.Ongpipattanakul, C.Volk, R.F.Chuo, S.W.Arkin, M.R.Renslo, A.R.Craik, C.S.

(2022) Cell Chem Biol 29: 785-798.e19

  • DOI: https://doi.org/10.1016/j.chembiol.2022.03.007
  • Primary Citation of Related Structures:  
    7TCZ

  • PubMed Abstract: 

    Viruses are responsible for some of the most deadly human diseases, yet available vaccines and antivirals address only a fraction of the potential viral human pathogens. Here, we provide a methodology for managing human herpesvirus (HHV) infection by covalently inactivating the HHV maturational protease via a conserved, non-catalytic cysteine (C161). Using human cytomegalovirus protease (HCMV Pr) as a model, we screened a library of disulfides to identify molecules that tether to C161 and inhibit proteolysis, then elaborated hits into irreversible HCMV Pr inhibitors that exhibit broad-spectrum inhibition of other HHV Pr homologs. We further developed an optimized tool compound targeted toward HCMV Pr and used an integrative structural biology and biochemical approach to demonstrate inhibitor stabilization of HCMV Pr homodimerization, exploiting a conformational equilibrium to block proteolysis. Irreversible HCMV Pr inhibition disrupts HCMV infectivity in cells, providing proof of principle for targeting proteolysis via a non-catalytic cysteine to manage viral infection.


  • Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Assemblin263Human betaherpesvirus 5Mutation(s): 6 
Gene Names: UL80
EC: 3.4.21.97
UniProt
Find proteins for P16753 (Human cytomegalovirus (strain AD169))
Explore P16753 
Go to UniProtKB:  P16753
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16753
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GIT (Subject of Investigation/LOI)
Query on GIT

Download Ideal Coordinates CCD File 
B [auth A][1-(2-oxopropyl)-4-phenyl-1H-1,2,3-triazol-5-yl]methyl benzylcarbamate
C20 H20 N4 O3
WXRQXWFHRZFFIN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.673α = 90
b = 51.673β = 90
c = 215.726γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

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 General Medical Sciences (NIH/NIGMS)United StatesP50 GM082250
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM104659

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2022-04-13
    Changes: Database references
  • Version 1.2: 2022-06-01
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description