5UF0 | pdb_00005uf0

BRD4_BD2-A-35165


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.201 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.180 (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 1.2 of the entry. See complete history

Literature

Fragment-Based, Structure-Enabled Discovery of Novel Pyridones and Pyridone Macrocycles as Potent Bromodomain and Extra-Terminal Domain (BET) Family Bromodomain Inhibitors.

Wang, L.Pratt, J.K.Soltwedel, T.Sheppard, G.S.Fidanze, S.D.Liu, D.Hasvold, L.A.Mantei, R.A.Holms, J.H.McClellan, W.J.Wendt, M.D.Wada, C.Frey, R.Hansen, T.M.Hubbard, R.Park, C.H.Li, L.Magoc, T.J.Albert, D.H.Lin, X.Warder, S.E.Kovar, P.Huang, X.Wilcox, D.Wang, R.Rajaraman, G.Petros, A.M.Hutchins, C.W.Panchal, S.C.Sun, C.Elmore, S.W.Shen, Y.Kati, W.M.McDaniel, K.F.

(2017) J Med Chem 60: 3828-3850

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00017
  • Primary Citation Related Structures: 
    5UEU, 5UEW, 5UEX, 5UEY, 5UEZ, 5UF0

  • PubMed Abstract: 

    Members of the BET family of bromodomain containing proteins have been identified as potential targets for blocking proliferation in a variety of cancer cell lines. A two-dimensional NMR fragment screen for binders to the bromodomains of BRD4 identified a phenylpyridazinone fragment with a weak binding affinity (1, K i = 160 μM). SAR investigation of fragment 1, aided by X-ray structure-based design, enabled the synthesis of potent pyridone and macrocyclic pyridone inhibitors exhibiting single digit nanomolar potency in both biochemical and cell based assays. Advanced analogs in these series exhibited high oral exposures in rodent PK studies and demonstrated significant tumor growth inhibition efficacy in mouse flank xenograft models.


  • Organizational Affiliation
    • AbbVie Inc. , 1 North Waukegan Road, North Chicago, Illinois 60064, United States.

Macromolecule Content 

  • Total Structure Weight: 13.02 kDa 
  • Atom Count: 1,103 
  • Modeled Residue Count: 108 
  • Deposited Residue Count: 109 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4109Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
PHAROS:  O60885
GTEx:  ENSG00000141867 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
89J

Query on 89J



Download:Ideal Coordinates CCD File
B [auth A]2-methyl-5-(methylamino)-6-phenylpyridazin-3(2H)-one
C12 H13 N3 O
ZRCCUVSDZQJQEX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free:  0.201 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.049α = 90
b = 73.03β = 90
c = 33.596γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
XDSdata reduction
SCALAdata scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2017-06-28 
  • Deposition Author(s): Park, C.H.

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-04-03
    Changes: Refinement description