9OJS | pdb_00009ojs

Crystal structure of TNF alpha in complex with compound 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.245 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Discovery of Orally Efficacious Bridged Piperazines as smTNF Modulators.

Bian, Z.Schmidt, R.G.Wilson, N.S.Duignan, D.B.Breinlinger, E.Dombrowski, A.W.Erdman, P.Foley, C.M.Friedman, M.Gfesser, G.A.Goess, C.A.Gomtsyan, A.Judge, R.A.Kikuchi, R.Koshman, Y.Liu, X.Longenecker, K.L.McClure, A.Sippy, K.Wetter, J.M.Stoffel, R.Vasudevan, A.

(2025) J Med Chem 68: 14357-14383

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00323
  • Primary Citation of Related Structures:  
    9OJO, 9OJS, 9OJY, 9OK6

  • PubMed Abstract: 

    Tumor necrosis factor α (TNFα) plays a critical role in inflammatory and autoimmune diseases. While biologic drugs have improved patient outcomes in conditions like rheumatoid arthritis by disrupting TNFα signaling, small molecule targeting has been challenging due to the strong TNF-receptor binding and difficulty in disrupting the TNF trimer. This research presents small molecule TNFα inhibitors with a novel bridged-piperazine core, developed through molecular dynamics simulation and scaffold hopping. The initial hit was optimized using structure-based design, leading to the discovery of a lead molecule with similar potency to the prototype but enhanced physicochemical properties. This lead demonstrated oral efficacy in a mouse glucose-6-phosphate isomerase-induced paw swelling model, comparable to the effects of a TNFα antibody. The estimated effective human dose is 200 mg once daily, highlighting the potential for clinical development of these compounds.


  • Organizational Affiliation
    • AbbVie Inc, North Chicago, Illinois 60064, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor
A, B, C
158Homo sapiensMutation(s): 0 
Gene Names: TNFTNFATNFSF2
UniProt & NIH Common Fund Data Resources
Find proteins for P01375 (Homo sapiens)
Explore P01375 
Go to UniProtKB:  P01375
PHAROS:  P01375
GTEx:  ENSG00000232810 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01375
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CB0 (Subject of Investigation/LOI)
Query on A1CB0

Download Ideal Coordinates CCD File 
D [auth B](6R,13R,14R)-10-fluoro-11-[2-(2-hydroxypropan-2-yl)pyrimidin-5-yl]-7H-6,14-methanopyrido[3',2':4,5]imidazo[1,2-b][2,5]benzodiazocin-5(14H)-one
C23 H19 F N6 O2
VPMAXCQXHCHKNY-KRWDZBQOSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.245 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.705α = 90
b = 81.592β = 90
c = 92.277γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing

Structure Validation

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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: 2025-07-23
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Database references
  • Version 1.2: 2025-08-27
    Changes: Database references