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 8RYS | pdb_00008rys

Human IL-1beta, unliganded


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 
    0.221 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8RYS

This is version 1.2 of the entry. See complete history. 

Literature

Ligandability Assessment of IL-1 beta by Integrated Hit Identification Approaches.

Vulpetti, A., Rondeau, J.M., Bellance, M.H., Blank, J., Boesch, R., Boettcher, A., Bornancin, F., Buhr, S., Connor, L.E., Dumelin, C.E., Esser, O., Hediger, M., Hintermann, S., Hommel, U., Koch, E., Lapointe, G., Leder, L., Lehmann, S., Lehr, P., Meier, P., Muller, L., Ostermeier, D., Ramage, P., Schiebel-Haddad, S., Smith, A.B., Stojanovic, A., Velcicky, J., Yamamoto, R., Hurth, K.

(2024) J Med Chem 67: 8141-8160

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00240
  • Primary Citation Related Structures: 
    8RYK, 8RYS, 8RZB

  • PubMed Abstract: 

    Human interleukin-1β (IL-1β) is a pro-inflammatory cytokine that plays a critical role in the regulation of the immune response and the development of various inflammatory diseases. In this publication, we disclose our efforts toward the discovery of IL-1β binders that interfere with IL-1β signaling. To this end, several technologies were used in parallel, including fragment-based screening (FBS), DNA-encoded library (DEL) technology, peptide discovery platform (PDP), and virtual screening. The utilization of distinct technologies resulted in the identification of new chemical entities exploiting three different sites on IL-1β, all of them also inhibiting the interaction with the IL-1R1 receptor. Moreover, we identified lysine 103 of IL-1β as a target residue suitable for the development of covalent, low-molecular-weight IL-1β antagonists.


  • Organizational Affiliation: 
    • Biomedical Research, Novartis, CH-4002 Basel, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 17.49 kDa 
  • Atom Count: 1,382 
  • Modeled Residue Count: 150 
  • Deposited Residue Count: 153 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-1 beta153Homo sapiensMutation(s): 0 
Gene Names: IL1B, IL1F2
UniProt & NIH Common Fund Data Resources
Find proteins for P01584 (Homo sapiens)
Explore P01584 
Go to UniProtKB:  P01584
PHAROS:  P01584
GTEx:  ENSG00000125538 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01584
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free:  0.221 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.784α = 90
b = 54.784β = 90
c = 76.173γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
Aimlessdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Database references
  • Version 1.2: 2024-06-05
    Changes: Database references