6X82

Crystal Structure of TNFalpha with isoquinoline compound 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UTM (Subject of Investigation/LOI)
Query on UTM

Download Ideal Coordinates CCD File 
G [auth A],
H [auth D]
8-[4-(2-{5-[(4-methylpiperazin-1-yl)methyl]-2-(1H-pyrrolo[3,2-c]pyridin-3-yl)phenoxy}ethyl)phenyl]isoquinoline
C36 H35 N5 O
KOBJJEIVOKWSMI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.902α = 90
b = 113.92β = 90
c = 120.73γ = 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