7AYR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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: 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 ...

    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

    Universidade de Lisboa Faculdade de Farmacia, Medicinal Chemistry, Av. Professor Gama Pinto, 1649-003, Lisboa, PORTUGAL.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dipeptidyl peptidase 8A, B898Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6V1X1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S9W (Subject of Investigation/LOI)
Query on S9W

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
~{N}-[3-[[4-[(4-bromophenyl)methyl]piperazin-1-yl]methyl]phenyl]-4-methanoyl-oxane-4-carboxamide
C25 H30 Br N3 O3
PPXXFRMHSKGYSK-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
TMO
Query on TMO

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
trimethylamine oxide
C3 H9 N O
UYPYRKYUKCHHIB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

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