9OJY | pdb_00009ojy

Crystal structure of TNF alpha in complex with compound 3.

PDB DOI: https://doi.org/10.2210/pdb9OJY/pdb

Classification: CYTOKINE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-05-08 Released: 2025-07-23
Deposition Author(s): Judge, R.A., Longenecker, K.L., Bian, Z.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.253 (Depositor), 0.278 (DCC)
R-Value Work:
0.215 (Depositor), 0.234 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

PubMed: 40632677 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.5c00323
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 105.97 kDa
Atom Count: 6,234
Modeled Residue Count: 794
Deposited Residue Count: 948
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor	A, B, C, D, E A, B, C, D, E, F	158	Homo sapiens	Mutation(s): 0 Gene Names: TNF, TNFA, TNFSF2
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01375
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CBZ (Subject of Investigation/LOI) Query on A1CBZ Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth D] MOL2 format, chain G [auth B] MOL2 format, chain H [auth D] mmCIF format, chain G [auth B] mmCIF format, chain H [auth D]	G [auth B], H [auth D]	(6R,13R,14S)-1-(difluoromethoxy)-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 C₂₄ H₂₀ F₂ N₆ O₃ PQIYTIQOQHGRFX-MRXNPFEDSA-N		Interactions Focus chain G [auth B] Focus chain H [auth D] Interactions & Density Focus chain G [auth B] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.253 (Depositor), 0.278 (DCC)
R-Value Work: 0.215 (Depositor), 0.234 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 251.546	α = 90
b = 65.589	β = 95.08
c = 54.416	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
autoPROC	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-23

Deposition Author(s):

Longenecker, K.L.

Funding Organization	Location	Grant 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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.