7ZXS

Crystal structure of DPP9 in complex with a 4-oxo-b-lactam based inhibitor, A295


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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 61: 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase 9
A, C
850Homo 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase 9
B, D
850Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KBO (Subject of Investigation/LOI)
Query on KBO

Download Ideal Coordinates CCD File 
AA [auth C],
E [auth A],
M [auth B],
MA [auth D]
2-ethyl-2-methanoyl-~{N}-[3-[[4-(quinolin-8-ylmethyl)piperazin-1-yl]methyl]phenyl]butanamide
C28 H34 N4 O2
HUVCJXYEGHNBRX-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
IA [auth C],
XA [auth D],
Y [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
F [auth A]
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
F [auth A],
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
HA [auth C],
I [auth A],
J [auth A],
JA [auth C],
K [auth A],
KA [auth C],
L [auth A],
LA [auth C],
N [auth B],
NA [auth D],
O [auth B],
OA [auth D],
P [auth B],
PA [auth D],
Q [auth B],
QA [auth D],
R [auth B],
RA [auth D],
S [auth B],
SA [auth D],
T [auth B],
TA [auth D],
U [auth B],
UA [auth D],
V [auth B],
VA [auth D],
W [auth B],
WA [auth D],
X [auth B],
YA [auth D],
Z [auth B],
ZA [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A, C
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.35α = 65.25
b = 106.176β = 70.43
c = 121.127γ = 75.86
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
X-GENdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release
  • Version 1.1: 2022-11-16
    Changes: Database references
  • Version 1.2: 2022-11-23
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description