9MDZ | pdb_00009mdz

anti-IL23R VHH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 
    0.159 (Depositor), 0.158 (DCC) 
  • R-Value Work: 
    0.145 (Depositor), 0.145 (DCC) 
  • R-Value Observed: 
    0.145 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9MDZ

This is version 1.1 of the entry. See complete history

Literature

Engineering a protease-stable, oral single-domain antibody to inhibit IL-23 signaling.

Ota, N.Davies, C.W.Kang, J.Yan, D.Scherl, A.Wong, A.Cook, R.Tao, X.Dunlap, D.Klabunde, S.Mantik, P.Mohanan, V.Lin, W.McBride, J.Sadekar, S.Storek, K.M.Lupardus, P.Ye, Z.Ackerly Wallweber, H.Kiefer, J.R.Xu, M.Chan, P.Nagapudi, K.Yi, T.Koerber, J.T.

(2025) Proc Natl Acad Sci U S A 122: e2501635122-e2501635122

  • DOI: https://doi.org/10.1073/pnas.2501635122
  • Primary Citation Related Structures: 
    9MDZ, 9MFG

  • PubMed Abstract: 

    Interleukin (IL)-23 is a validated therapeutic target in inflammatory bowel disease. While antibodies targeting IL23 demonstrate clinical efficacy, they face challenges such as high costs, safety risks, and the necessity of parenteral administration. Here, we present a workflow to simultaneously enhance the affinity and protease stability of an inhibitory anti-IL23R VHH for oral use. Cocrystal structure analysis reveals that the anti-IL23R VHH employs both CDR and framework residues to achieve picomolar affinity for IL23R. The engineered VHH remains stable for over 8 h in intestinal fluid and 24 h in fecal samples. Oral administration of this VHH achieves deep pathway inhibition in a murine colitis model. Furthermore, a single pill provides sustained IL23R inhibition in nonhuman primate blood for over 24 h. With high potency, gut stability, high production yield, and favorable drug-like properties, oral VHHs offer a promising approach for inflammatory bowel diseases.


  • Organizational Affiliation
    • Department of Immunology Discovery, Genentech, South San Francisco, CA 94080.

Macromolecule Content 

  • Total Structure Weight: 13.32 kDa 
  • Atom Count: 1,248 
  • Modeled Residue Count: 120 
  • Deposited Residue Count: 120 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
anti-IL23R VHHA [auth E]120Lama glamaMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free:  0.159 (Depositor), 0.158 (DCC) 
  • R-Value Work:  0.145 (Depositor), 0.145 (DCC) 
  • R-Value Observed: 0.145 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.615α = 90
b = 125.615β = 90
c = 41.563γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Database references