7SVL

DPP9 IN COMPLEX WITH LIGAND ICeD-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 
    0.341 (Depositor), 0.340 (DCC) 
  • R-Value Work: 
    0.263 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 
    0.264 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted D06Click on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

A Phenotypic Screen Identifies Potent DPP9 Inhibitors Capable of Killing HIV-1 Infected Cells.

Moore, K.P.Schwaid, A.G.Tudor, M.Park, S.Beshore, D.C.Converso, A.Shipe, W.D.Anand, R.Lan, P.Moningka, R.Rothman, D.M.Sun, W.Chi, A.Cornella-Taracido, I.Adam, G.C.Bahnck-Teets, C.Carroll, S.S.Fay, J.F.Goh, S.L.Lusen, J.Quan, S.Rodriguez, S.Xu, M.Andrews, C.L.Song, C.Filzen, T.Li, J.Hollenstein, K.Klein, D.J.Lammens, A.Lim, U.M.Fang, Z.McHale, C.Li, Y.Lu, M.Diamond, T.L.Howell, B.J.Zuck, P.Balibar, C.J.

(2022) ACS Chem Biol 17: 2595-2604

  • DOI: https://doi.org/10.1021/acschembio.2c00515
  • Primary Citation of Related Structures:  
    7SVL, 7SVM, 7SVN, 7SVO

  • PubMed Abstract: 

    Although current antiretroviral therapy can control HIV-1 replication and prevent disease progression, it is not curative. Identifying mechanisms that can lead to eradication of persistent viral reservoirs in people living with HIV-1 (PLWH) remains an outstanding challenge to achieving cure. Utilizing a phenotypic screen, we identified a novel chemical class capable of killing HIV-1 infected peripheral blood mononuclear cells. Tool compounds ICeD-1 and ICeD-2 (" i nducer of ce ll d eath-1 and 2"), optimized for potency and selectivity from screening hits, were used to deconvolute the mechanism of action using a combination of chemoproteomic, biochemical, pharmacological, and genetic approaches. We determined that these compounds function by modulating dipeptidyl peptidase 9 (DPP9) and activating the caspase recruitment domain family member 8 (CARD8) inflammasome. Efficacy of ICeD-1 and ICeD-2 was dependent on HIV-1 protease activity and synergistic with efavirenz, which promotes premature activation of HIV-1 protease at high concentrations in infected cells. This in vitro synergy lowers the efficacious cell kill concentration of efavirenz to a clinically relevant dose at concentrations of ICeD-1 or ICeD-2 that do not result in complete DPP9 inhibition. These results suggest engagement of the pyroptotic pathway as a potential approach to eliminate HIV-1 infected cells.


  • Organizational Affiliation

    Chemical Biology, Merck & Co., Inc., Rahway, New Jersey 07065, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase 9
A, B, C, D
869Homo sapiensMutation(s): 0 
Gene Names: DPP9DPRP2
EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q86TI2 (Homo sapiens)
Explore Q86TI2 
Go to UniProtKB:  Q86TI2
PHAROS:  Q86TI2
GTEx:  ENSG00000142002 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86TI2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free:  0.341 (Depositor), 0.340 (DCC) 
  • R-Value Work:  0.263 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 0.264 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.716α = 90
b = 117.398β = 105.6
c = 163.691γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted D06Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-05
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description