4GAF

Crystal structure of EBI-005, a chimera of human IL-1beta and IL-1Ra, bound to human Interleukin-1 receptor type 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Design of a superior cytokine antagonist for topical ophthalmic use.

Hou, J.Townson, S.A.Kovalchin, J.T.Masci, A.Kiner, O.Shu, Y.King, B.M.Schirmer, E.Golden, K.Thomas, C.Garcia, K.C.Zarbis-Papastoitsis, G.Furfine, E.S.Barnes, T.M.

(2013) Proc.Natl.Acad.Sci.USA 110: 3913-3918

  • DOI: 10.1073/pnas.1217996110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • IL-1 is a key inflammatory and immune mediator in many diseases, including dry-eye disease, and its inhibition is clinically efficacious in rheumatoid arthritis and cryopyrin-associated periodic syndromes. To treat ocular surface disease with a topic ...

    IL-1 is a key inflammatory and immune mediator in many diseases, including dry-eye disease, and its inhibition is clinically efficacious in rheumatoid arthritis and cryopyrin-associated periodic syndromes. To treat ocular surface disease with a topical biotherapeutic, the uniqueness of the site necessitates consideration of the agent's size, target location, binding kinetics, and thermal stability. Here we chimerized two IL-1 receptor ligands, IL-1β and IL-1Ra, to create an optimized receptor antagonist, EBI-005, for topical ocular administration. EBI-005 binds its target, IL-1R1, 85-fold more tightly than IL-1Ra, and this increase translates to an ∼100-fold increase in potency in vivo. EBI-005 preserves the affinity bias of IL-1Ra for IL-1R1 over the decoy receptor (IL-1R2), and, surprisingly, is also more thermally stable than either parental molecule. This rationally designed antagonist represents a unique approach to therapeutic design that can potentially be exploited for other β-trefoil family proteins in the IL-1 and FGF families.


    Organizational Affiliation

    Eleven Biotherapeutics, Inc., Cambridge, MA 02142, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EBI-005
A
153Homo sapiensMutation(s): 0 
Gene Names: IL1B (IL1F2)
Find proteins for P01584 (Homo sapiens)
Go to Gene View: IL1B
Go to UniProtKB:  P01584
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Interleukin-1 receptor type 1
B
319Homo sapiensMutation(s): 0 
Gene Names: IL1R1 (IL1R, IL1RA, IL1RT1)
Find proteins for P14778 (Homo sapiens)
Go to Gene View: IL1R1
Go to UniProtKB:  P14778
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.215 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 60.350α = 90.00
b = 149.270β = 90.00
c = 126.170γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
PHASERphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2013-03-27
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description