9MFG | pdb_00009mfg

Complex of IL23 receptor and VHH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.246 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9MFG

Ligand Structure Quality Assessment 


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: 202.84 kDa 
  • Atom Count: 13,510 
  • Modeled Residue Count: 1,648 
  • Deposited Residue Count: 1,696 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-23 receptor
A, B, C, D
304Homo sapiensMutation(s): 0 
Gene Names: IL23R
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VWK5 (Homo sapiens)
Explore Q5VWK5 
Go to UniProtKB:  Q5VWK5
PHAROS:  Q5VWK5
GTEx:  ENSG00000162594 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5VWK5
Glycosylation
Glycosylation Sites: 4Go to GlyGen: Q5VWK5-1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
VHH
E, F, G, H
120Lama glamaMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
I, T
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB
GlyCosmos: G21290RB
GlyGen: G21290RB
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J, N, Q, R, U
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
K, O
4N-Glycosylation
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
L, P, S
4N-Glycosylation
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
M
3N-Glycosylation

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth D],
V [auth A],
W [auth A],
Y [auth B],
Z [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
FA [auth E],
GA [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
EA [auth E]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
SCN

Query on SCN



Download:Ideal Coordinates CCD File
BA [auth D],
CA [auth D],
DA [auth D],
HA [auth G],
X [auth A]
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.246 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.313α = 90
b = 403.472β = 90
c = 84.247γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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