8UUI | pdb_00008uui

X-ray structure of Interleukin-23 in complex with peptide 23-446


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 
    0.278 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification of an Induced Orthosteric Pocket in IL-23: A New Avenue for Non-biological Therapeutic Targeting.

Lecomte, F.C.Joseph, J.S.Stalewski, J.Shen, Q.Arnoult, E.Sridhar, V.Liu, M.Hu, Y.Gasendo, J.G.Ben Arie, H.Keinan, N.Keidar, L.Aviv, I.Ruvinov, E.Grandjean, J.Dores-Silva, P.R.Mak, A.Santoso, B.Kim, S.Shende, V.Wever, W.J.Mirzadegan, T.Zhu, Z.Fuchs, B.Pinton, P.Szabady, R.

(2025) ACS Chem Biol 20: 1609-1618

  • DOI: https://doi.org/10.1021/acschembio.5c00181
  • Primary Citation of Related Structures:  
    8UUI

  • PubMed Abstract: 

    Interleukin 23 (IL23) is a key driver of autoimmune inflammatory pathology and has been successfully targeted by therapeutic antibodies for the treatment of psoriasis and ulcerative colitis. Identifying small-molecule inhibitors of IL23 signaling is of potential interest for drug development. We report the identification of an induced-fit orthosteric binding pocket on the IL23p19 subunit that may be suitable for small-molecule inhibition. X-ray crystallography was used to determine the structure of the IL23 heterodimer when bound to inhibitory peptide 23-446 and to confirm peptide binding to the IL23p19 subunit at the location of its interface with the IL23 receptor (IL23R). We then applied structure-based design to modify peptide 23-446. This process involved identifying key residues responsible for inhibitory activity and generating structure-activity relationship-optimized peptides with low nanomolar affinity for IL-23 and corresponding inhibitory potency against IL-23R binding. These optimized peptides show promise as potential therapeutic candidates in their own right and may also serve as valuable starting points for further discovery. The most potent of these peptides was used to develop a fluorescence polarization probe and to design a high-throughput screening assay, which was validated through a pilot screen using a small fragment-based compound library. This screening strategy has the potential to support the discovery of peptides or small molecules that bind to the orthosteric pocket, thereby blocking the IL-23R interaction and downstream signaling.


  • Organizational Affiliation
    • Ferring Research Institute, 4245 Sorrento Valley Blvd, San Diego, California CA92121, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-23 subunit alphaA [auth B]176Homo sapiensMutation(s): 0 
Gene Names: IL23A
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPF7 (Homo sapiens)
Explore Q9NPF7 
Go to UniProtKB:  Q9NPF7
PHAROS:  Q9NPF7
GTEx:  ENSG00000110944 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NPF7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-12 subunit betaB [auth A]307Homo sapiensMutation(s): 0 
Gene Names: IL12BNKSF2
UniProt & NIH Common Fund Data Resources
Find proteins for P29460 (Homo sapiens)
Explore P29460 
Go to UniProtKB:  P29460
PHAROS:  P29460
GTEx:  ENSG00000113302 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29460
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P29460-1
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
peptide 23-446C [auth D]20unidentifiedMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth C]4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free:  0.278 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.74α = 90
b = 110.74β = 90
c = 85.51γ = 120
Software Package:
Software NamePurpose
autoPROCdata processing
PHENIXphasing
PHENIXrefinement
Cootmodel building
XDSdata reduction
pointlessdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release
  • Version 1.1: 2025-07-30
    Changes: Database references