Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, B115

Experimental Data Snapshot

  • Resolution: 2.69 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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Chemoproteomics-Enabled Identification of 4-Oxo-beta-Lactams as Inhibitors of Dipeptidyl Peptidases 8 and 9.

Carvalho, L.A.R.Ross, B.Fehr, L.Bolgi, O.Wohrle, S.Lum, K.M.Podlesainski, D.Vieira, A.C.Kiefersauer, R.Felix, R.Rodrigues, T.Lucas, S.D.Gross, O.Geiss-Friedlander, R.Cravatt, B.F.Huber, R.Kaiser, M.Moreira, R.

(2022) Angew Chem Int Ed Engl : e202210498-e202210498

  • DOI: https://doi.org/10.1002/anie.202210498
  • Primary Citation of Related Structures:  
    7A3G, 7A3J, 7A3L, 7AYQ, 7AYR, 7OR4, 7OZ7, 7ZXS

  • PubMed Abstract: 

    Dipeptidyl peptidases 8 and 9 (DPP8/9) have gathered interest as drug targets due to their important roles in biological processes like immunity and tumorigenesis. Elucidation of their distinct individual functions remains an ongoing task and could benefit from the availability of novel, chemically diverse and selective chemical tools. Here, we report the activity-based protein profiling (ABPP)-mediated discovery of 4-oxo-β-lactams as potent, non-substrate-like nanomolar DPP8/9 inhibitors. X-ray crystallographic structures revealed different ligand binding modes for DPP8 and DPP9, including an unprecedented targeting of an extended S2' (eS2') subsite in DPP8. Biological assays confirmed inhibition at both target and cellular levels. Altogether, our integrated chemical proteomics and structure-guided small molecule design approach led to novel DPP8/9 inhibitors with alternative molecular inhibition mechanisms, delivering the highest selectivity index reported to date.

  • Organizational Affiliation

    Department of Pharmaceutical Sciences and Medicines, Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase 8
A, B
898Homo sapiensMutation(s): 0 
Gene Names: DPP8DPRP1MSTP097MSTP135MSTP141
UniProt & NIH Common Fund Data Resources
Find proteins for Q6V1X1 (Homo sapiens)
Explore Q6V1X1 
Go to UniProtKB:  Q6V1X1
GTEx:  ENSG00000074603 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6V1X1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.69 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.563α = 90
b = 149.563β = 90
c = 269.633γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2022-09-28
    Changes: Database references
  • Version 1.2: 2022-11-16
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description