5LPK

Crystal structure of the bromodomain of human EP300 bound to the inhibitor XDM1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Beyond the BET Family: Targeting CBP/p300 with 4-Acyl Pyrroles.

Hugle, M.Lucas, X.Ostrovskyi, D.Regenass, P.Gerhardt, S.Einsle, O.Hau, M.Jung, M.Breit, B.Gunther, S.Wohlwend, D.

(2017) Angew. Chem. Int. Ed. Engl. 56: 12476-12480

  • DOI: 10.1002/anie.201705516
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bromodomain and extra-terminal domain (BET) inhibitors are widely used both as chemical tools to study the biological role of their targets in living organisms and as candidates for drug development against several cancer variants and human disorders ...

    Bromodomain and extra-terminal domain (BET) inhibitors are widely used both as chemical tools to study the biological role of their targets in living organisms and as candidates for drug development against several cancer variants and human disorders. However, non-BET bromodomains such as those in p300 and CBP are less studied. XDM-CBP is a highly potent and selective inhibitor for the bromodomains of CBP and p300 derived from a pan-selective BET BRD-binding fragment. Along with X-ray crystal-structure analysis and thermodynamic profiling, XDM-CBP was used in screenings of several cancer cell lines in vitro to study its inhibitory potential on cancer cell proliferation. XDM-CBP is demonstrated to be a potent and selective CBP/p300 inhibitor that acts on specific cancer cell lines, in particular malignant melanoma, breast cancer, and leukemia.


    Organizational Affiliation

    Freiburg Institute for Advanced Studies (FRIAS), Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany.,Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 9, 79104, Freiburg, Germany.,Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany.,Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany.,School of Life Sciences, Division of Biological Chemistry and Drug Discovery, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone acetyltransferase p300
A, B, C, D, E, F, G
122Homo sapiensMutation(s): 0 
Gene Names: EP300 (P300)
EC: 2.3.1.48
Find proteins for Q09472 (Homo sapiens)
Go to Gene View: EP300
Go to UniProtKB:  Q09472
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, C, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
XDM
Query on XDM

Download SDF File 
Download CCD File 
A, B, C, D, E, F
~{N}-[(3-chlorophenyl)methyl]-4-ethanoyl-3-ethyl-5-methyl-1~{H}-pyrrole-2-carboxamide
XDM1
C17 H19 Cl N2 O2
KHTPXNJKROZWBI-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XDMKd: 3060 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 133.600α = 90.00
b = 61.040β = 98.31
c = 135.680γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyWO2012/1-1

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-10-11
    Type: Database references