9HYT | pdb_00009hyt

Crystal structure of the GFRaL receptor in complex with an inhibitory cyclic peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.244 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.201 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9HYT

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Design of Bicyclic Peptide Tandems Mimicking the Homodimeric GDF15 Protein to Inhibit GDF15-GFRaL-RET Complex Cell Signaling.

Noisier, A.F.M.Sandmark, J.Edfeldt, F.Backmark, A.Broddefalk, J.Wandzik, J.Jurva, U.Ek, M.Johansson, C.A.Barlind, L.Gunnarsson, J.Bigalke, J.M.Xue, Y.Frolov, A.I.Kankkonen, C.Roth, R.G.Fritsch, M.Watcham, S.van Rietschoten, K.Mudd, G.E.Harrison, H.Chen, L.Skynner, M.J.Craik, D.J.Chankeshwara, S.V.Lemurell, M.

(2025) J Med Chem 68: 21441-21457

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01378
  • Primary Citation Related Structures: 
    9HYT

  • PubMed Abstract: 

    The GDF15-GFRaL-RET signaling complex is involved in a broad range of disease states, with agonistic action of GDF15 affecting metabolism and body weight control, while inhibition is indicated in cancer and wasting disorders like cachexia. Here, we describe the discovery of the peptide inhibitors of the GDF15-GFRaL protein-protein interaction to prevent RET-induced signaling using both a structure-guided design and a phage display approach. Phage display provided bicyclic peptide hits with high affinity for GFRaL, and these were dimerized to mimic the bidentate interaction of homodimeric GDF15. Guided by structural data, the monomeric peptides were converted into tandem Bicycle molecules with picomolar affinities, similar to that of the endogenous GDF15 ligand. These dimerized protein mimetics inhibited cell signaling in a functional assay and showed improved pharmacokinetic properties compared with their monomeric counterparts. This is the first example of a homodimeric Bicycle molecule inhibiting receptor complex formation, thereby antagonizing the intracellular signaling response.


  • Organizational Affiliation
    • BicycleTx Limited, Portway Building, Granta Park, Cambridge CB21 6GS, U.K.

Macromolecule Content 

  • Total Structure Weight: 89.87 kDa 
  • Atom Count: 5,382 
  • Modeled Residue Count: 641 
  • Deposited Residue Count: 786 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GDNF family receptor alpha-like
A, B, C
245Homo sapiensMutation(s): 0 
Gene Names: GFRALC6orf144UNQ9356/PRO34128
UniProt & NIH Common Fund Data Resources
Find proteins for Q6UXV0 (Homo sapiens)
Explore Q6UXV0 
Go to UniProtKB:  Q6UXV0
PHAROS:  Q6UXV0
GTEx:  ENSG00000187871 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6UXV0
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Inhibitory cyclic peptide
D, E, F
17synthetic constructMutation(s): 0 

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
29N
(Subject of Investigation/LOI)

Query on 29N



Download:Ideal Coordinates CCD File
O [auth D],
P [auth E],
Q [auth F]
1,1',1''-(1,3,5-triazinane-1,3,5-triyl)tripropan-1-one
C12 H21 N3 O3
AEPJNZPJFYDQLM-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
J [auth B]
K [auth B]
L [auth B]
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth C],
N [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACY

Query on ACY



Download:Ideal Coordinates CCD File
I [auth B]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.244 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.201 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.541α = 90
b = 148.183β = 90
c = 198.053γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release
  • Version 1.1: 2025-10-29
    Changes: Database references
  • Version 1.2: 2025-11-05
    Changes: Database references