8RZB

IL-1beta in complex with covalent DEL hit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-1 beta
A, B, C, D
153Homo sapiensMutation(s): 0 
Gene Names: IL1BIL1F2
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H4A (Subject of Investigation/LOI)
Query on A1H4A

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth D]
8-[4-methyl-3-(trifluoromethyl)phenyl]-2-[[(7S)-7-(2-morpholin-4-ylethylcarbamoyl)-4-(phenylsulfonyl)-1,4-diazepan-1-yl]carbonyl]imidazo[1,2-a]pyridine-6-carboxylic acid
C35 H37 F3 N6 O7 S
CYRHEZSFDUZNDQ-PMERELPUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.479α = 72.88
b = 56.407β = 71.8
c = 67.792γ = 84.32
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

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