6Y8K

Crystal structure of CD137 in complex with the cyclic peptide BCY10916

• PDB DOI: https://doi.org/10.2210/pdb6Y8K/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2020-03-05 Released: 2021-02-03 
• Deposition Author(s): Upadhyaya, P., Kublin, J., Dods, R., Kristensson, J., Lahdenranta, J., Kleyman, M., Repash, E., Ma, J., Mudd, G., Van Rietschoten, K., Haines, E., Harrison, H., Beswick, P., Chen, L., McDonnell, K., Battula, S., Hurov, K., Keen, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.314 
• R-Value Work: 0.283 

Literature

Anticancer immunity induced by a synthetic tumor-targeted CD137 agonist.

Upadhyaya, P., Lahdenranta, J., Hurov, K., Battula, S., Dods, R., Haines, E., Kleyman, M., Kristensson, J., Kublin, J., Lani, R., Ma, J., Mudd, G., Repash, E., Van Rietschoten, K., Stephen, T., You, F., Harrison, H., Chen, L., McDonnell, K., Brandish, P., Keen, N.

(2021) J Immunother Cancer 9

• PubMed: 33500260 
• DOI: https://doi.org/10.1136/jitc-2020-001762
• Primary Citation of Related Structures:  
  6Y8K


• PubMed Abstract: 
  

  In contrast to immune checkpoint inhibitors, the use of antibodies as agonists of immune costimulatory receptors as cancer therapeutics has largely failed. We sought to address this problem using a new class of modular synthetic drugs, termed tumor-targeted immune cell agonists (TICAs), based on constrained bicyclic peptides ( Bicycles ).

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Organizational Affiliation: 

Bicycle Therapeutics, Lexington, Massachusetts, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 20.21 kDa 
• Atom Count: 1,144 
• Modelled Residue Count: 145 
• Deposited Residue Count: 180 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor receptor superfamily member 9	A [auth AAA]	165	Homo sapiens	Mutation(s): 0  Gene Names: TNFRSF9, CD137, ILA
UniProt & NIH Common Fund Data Resources
Find proteins for Q07011 (Homo sapiens) Explore Q07011  Go to UniProtKB:  Q07011
PHAROS:  Q07011 GTEx:  ENSG00000049249

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BCY10916	B [auth PPP]	15	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
29N (Subject of Investigation/LOI)	I [auth PPP]	1,1',1''-(1,3,5-triazinane-1,3,5-triyl)tripropan-1-one C12 H21 N3 O3 AEPJNZPJFYDQLM-UHFFFAOYSA-N
SO4	E [auth AAA], F [auth AAA], G [auth AAA]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth AAA]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	C [auth AAA]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	H [auth AAA]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NLE	B [auth PPP]	L-PEPTIDE LINKING	C6 H13 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.314 
• R-Value Work: 0.283 
• Space Group: P 4₂ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.47	α = 90
b = 122.47	β = 90
c = 122.47	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-03 
Deposition Author(s): Upadhyaya, P., Kublin, J., Dods, R., Kristensson, J., Lahdenranta, J., Kleyman, M., Repash, E., Ma, J., Mudd, G., Van Rietschoten, K., Haines, E., Harrison, H., Beswick, P., Chen, L., McDonnell, K., Battula, S., Hurov, K., Keen, N.

Revision History  

• Version 1.0: 2021-02-03
  Type: Initial release
  
• Version 1.1: 2021-02-10
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description