Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 24.35 kDa 
• Atom Count: 1633 
• Modelled Residue Count: 193 
• Deposited Residue Count: 211 
• Unique protein chains: 2

6RW2

Bicycle Toxin Conjugate bound to EphA2

• PDB DOI: 10.2210/pdb6RW2/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-06-03 Released: 2020-04-08 
• Deposition Author(s): Brown, D.G., Schroeder, S., Chen, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.265 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 

Literature

Identification and Optimization of EphA2-Selective Bicycles for the Delivery of Cytotoxic Payloads.

Mudd, G.E., Brown, A., Chen, L., van Rietschoten, K., Watcham, S., Teufel, D.P., Pavan, S., Lani, R., Huxley, P., Bennett, G.S.

(2020) J Med Chem 63: 4107-4116

• PubMed: 32202781 
• DOI: 10.1021/acs.jmedchem.9b02129
• Primary Citation of Related Structures:  
  6RW2


• PubMed Abstract: 
  

Bicycles are constrained bicyclic peptides that represent a promising binding modality for use in targeted drug conjugates. A phage display screen against EphA2, a receptor tyrosine kinase highly expressed in a number of solid tumors, identified a number of Bicycle families with low nanomolar affinity. A Bicycle toxin conjugate (BTC) was generated by derivatization of one of these Bicycles with the potent cytotoxin DM1 via a cleavable linker. This BTC demonstrated potent antitumor activity in vivo but was poorly tolerated, which was hypothesized to be the result of undesired liver uptake caused by poor physicochemical properties. Chemical optimization of a second Bicycle, guided by structural biology, provided a high affinity, metabolically stable Bicycle with improved physicochemical properties. A BTC incorporating this Bicycle also demonstrated potent antitumor activity and was very well tolerated when compared to the initial BTC. Phage display selection followed by chemical optimization of Bicycles can deliver potent drug conjugates with favorable pharmaceutical properties.

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Organizational Affiliation: 

BicycleTx Limited, Building 900, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ephrin type-A receptor 2	A	193	Homo sapiens	Mutation(s): 0  Gene Names: EPHA2, ECK EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P29317 (Homo sapiens) Explore P29317  Go to UniProtKB:  P29317
PHAROS:  P29317

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ALA-ARG-ASP-CYS-PRO-LEU-VAL-ASN-PRO-LEU-CYS-LEU-HIS-PRO-GLY-TRP-THR-CYS	B	18	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
29N (Subject of Investigation/LOI)	D [auth B]	1,1',1''-(1,3,5-triazinane-1,3,5-triyl)tripropan-1-one C12 H21 N3 O3 AEPJNZPJFYDQLM-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.265 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.09	α = 90
b = 113.68	β = 90
c = 130.96	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-06-03 
• Released Date: 2020-04-08 
Deposition Author(s): Brown, D.G., Schroeder, S., Chen, L.

Revision History  

• Version 1.0: 2020-04-08
  Type: Initial release
  
• Version 1.1: 2020-04-22
  Changes: Database references
• Version 1.2: 2020-05-06
  Changes: Database references