6ZCI

Crystal structure of BRD4-BD1 in complex with NVS-BET-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

BET bromodomain inhibitors regulate keratinocyte plasticity.

Schutzius, G.Kolter, C.Bergling, S.Tortelli, F.Fuchs, F.Renner, S.Guagnano, V.Cotesta, S.Rueeger, H.Faller, M.Bouchez, L.Salathe, A.Nigsch, F.Richards, S.M.Louis, M.Gruber, V.Aebi, A.Turner, J.Grandjean, F.Li, J.Dimitri, C.Thomas, J.R.Schirle, M.Blank, J.Drueckes, P.Vaupel, A.Tiedt, R.Manley, P.W.Klopp, J.Hemmig, R.Zink, F.Leroy, N.Carbone, W.Roma, G.Keller, C.G.Dales, N.Beyerbach, A.Zimmerlin, A.Bonenfant, D.Terranova, R.Berwick, A.Sahambi, S.Reynolds, A.Jennings, L.L.Ruffner, H.Tarsa, P.Bouwmeester, T.Driver, V.Frederiksen, M.Lohmann, F.Kirkland, S.

(2021) Nat Chem Biol 17: 280-290

  • DOI: https://doi.org/10.1038/s41589-020-00716-z
  • Primary Citation of Related Structures:  
    6ZCI

  • PubMed Abstract: 

    Although most acute skin wounds heal rapidly, non-healing skin ulcers represent an increasing and substantial unmet medical need that urgently requires effective therapeutics. Keratinocytes resurface wounds to re-establish the epidermal barrier by transitioning to an activated, migratory state, but this ability is lost in dysfunctional chronic wounds. Small-molecule regulators of keratinocyte plasticity with the potential to reverse keratinocyte malfunction in situ could offer a novel therapeutic approach in skin wound healing. Utilizing high-throughput phenotypic screening of primary keratinocytes, we identify such small molecules, including bromodomain and extra-terminal domain (BET) protein family inhibitors (BETi). BETi induce a sustained activated, migratory state in keratinocytes in vitro, increase activation markers in human epidermis ex vivo and enhance skin wound healing in vivo. Our findings suggest potential clinical utility of BETi in promoting keratinocyte re-epithelialization of skin wounds. Importantly, this novel property of BETi is exclusively observed after transient low-dose exposure, revealing new potential for this compound class.


  • Organizational Affiliation

    Novartis Institutes for BioMedical Research, Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4148Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QFN (Subject of Investigation/LOI)
Query on QFN

Download Ideal Coordinates CCD File 
B [auth A](4~{R})-4-(4-chlorophenyl)-1-cyclopropyl-5-(1,5-dimethyl-6-oxidanylidene-pyridin-3-yl)-3-methyl-4~{H}-pyrrolo[3,4-c]pyrazol-6-one
C22 H21 Cl N4 O2
PXGREUPWZAUELV-LJQANCHMSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.615α = 90
b = 44.058β = 90
c = 80.552γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2020-12-23 
  • Deposition Author(s): Faller, M.

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Database references
  • Version 1.2: 2021-03-03
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description