7SVM

DPP8 IN COMPLEX WITH LIGAND ICeD-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 8
A, B, C
898Homo sapiensMutation(s): 0 
Gene Names: DPP8DPRP1MSTP097MSTP135MSTP141
EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q6V1X1 (Homo sapiens)
Explore Q6V1X1 
Go to UniProtKB:  Q6V1X1
PHAROS:  Q6V1X1
GTEx:  ENSG00000074603 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6V1X1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D06 (Subject of Investigation/LOI)
Query on D06

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
P [auth B],
Q [auth B],
R [auth B],
V [auth C],
W [auth C],
X [auth C]
(2S)-2-amino-1-(1,3-dihydro-2H-isoindol-2-yl)-2-[(1r,4S)-4-(pyrrolidin-1-yl)cyclohexyl]ethan-1-one
C20 H29 N3 O
SYXDQNGJEXFDND-SNRMKQJTSA-N
TMO
Query on TMO

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
K [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
S [auth B],
T [auth B],
U [auth B],
Y [auth C],
Z [auth C]
trimethylamine oxide
C3 H9 N O
UYPYRKYUKCHHIB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.288α = 90
b = 244.937β = 90
c = 261.487γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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