6X85 | pdb_00006x85

Crystal Structure of TNFalpha with indolinone compound 9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.252 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Development of Orally Efficacious Allosteric Inhibitors of TNF alpha via Fragment-Based Drug Design.

Dietrich, J.D.Longenecker, K.L.Wilson, N.S.Goess, C.Panchal, S.C.Swann, S.L.Petros, A.M.Hobson, A.D.Ihle, D.Song, D.Richardson, P.Comess, K.M.Cox, P.B.Dombrowski, A.Sarris, K.Donnelly-Roberts, D.L.Duignan, D.B.Gomtsyan, A.Jung, P.Krueger, A.C.Mathieu, S.McClure, A.Stoll, V.S.Wetter, J.Mankovich, J.A.Hajduk, P.J.Vasudevan, A.Stoffel, R.H.Sun, C.

(2021) J Med Chem 64: 417-429

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01280
  • Primary Citation Related Structures: 
    6X81, 6X82, 6X83, 6X85, 6X86

  • PubMed Abstract: 

    Tumor necrosis factor α (TNFα) is a soluble cytokine that is directly involved in systemic inflammation through the regulation of the intracellular NF-κB and MAPK signaling pathways. The development of biologic drugs that inhibit TNFα has led to improved clinical outcomes for patients with rheumatoid arthritis and other chronic autoimmune diseases; however, TNFα has proven to be difficult to drug with small molecules. Herein, we present a two-phase, fragment-based drug discovery (FBDD) effort in which we first identified isoquinoline fragments that disrupt TNFα ligand-receptor binding through an allosteric desymmetrization mechanism as observed in high-resolution crystal structures. The second phase of discovery focused on the de novo design and optimization of fragments with improved binding efficiency and drug-like properties. The 3-indolinone-based lead presented here displays oral, in vivo efficacy in a mouse glucose-6-phosphate isomerase (GPI)-induced paw swelling model comparable to that seen with a TNFα antibody.


  • Organizational Affiliation
    • Research & Development, AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064, United States.

Macromolecule Content 

  • Total Structure Weight: 105.33 kDa 
  • Atom Count: 6,599 
  • Modeled Residue Count: 842 
  • Deposited Residue Count: 948 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tumor necrosis factor
A, B, C, D, E
A, B, C, D, E, F
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
UTV
(Subject of Investigation/LOI)

Query on UTV



Download:Ideal Coordinates CCD File
G [auth B]1-{[2-(difluoromethoxy)phenyl]methyl}-2,2-dimethyl-1,2-dihydro-3H-indol-3-one
C18 H17 F2 N O2
BSVSFPVFEQPRJW-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
UTV BindingDB:  6X85 Kd: 1.90e+4 (nM) from 1 assay(s)
IC50: 5300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.252 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 252.508α = 90
b = 65.672β = 95.1
c = 54.241γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary