5LPK

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

• PDB DOI: https://doi.org/10.2210/pdb5LPK/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-08-13 Released: 2017-08-16 
• Deposition Author(s): Huegle, M., Wohlwend, D.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.203 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Starting Model: experimental

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

• PubMed: 28766825 
• DOI: https://doi.org/10.1002/anie.201705516
• Primary Citation of Related Structures:  
  5LPJ, 5LPK, 5LPL, 5LPM, 5NRW, 5NU3, 5NU5


• 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. 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.

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Organizational Affiliation: 

Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 6 assigned by authors.

Biological Assembly 7  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 7 assigned by authors.

Macromolecule Content

• Total Structure Weight: 105.14 kDa 
• Atom Count: 7,515 
• Modelled Residue Count: 799 
• Deposited Residue Count: 854 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase p300	A, B, C, D, E, F, G	122	Homo sapiens	Mutation(s): 0  Gene Names: EP300, P300 EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q09472 (Homo sapiens) Explore Q09472  Go to UniProtKB:  Q09472
PHAROS:  Q09472 GTEx:  ENSG00000100393

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XDM	AA [auth D], EA [auth E], FA [auth E], H [auth A], IA [auth F], P [auth B], X [auth C]	~{N}-[(3-chlorophenyl)methyl]-4-ethanoyl-3-ethyl-5-methyl-1~{H}-pyrrole-2-carboxamide C17 H19 Cl N2 O2 KHTPXNJKROZWBI-UHFFFAOYSA-N
PG4	W [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4	GA [auth E], I [auth A], J [auth A], JA [auth F], Y [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	BA [auth D], CA [auth D], DA [auth D], HA [auth E], K [auth A], KA [auth F], L [auth A], LA [auth F], M [auth A], MA [auth G], N [auth A], O [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], Z [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.203 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.6	α = 90
b = 61.04	β = 98.31
c = 135.68	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Huegle, M., Wohlwend, D.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	WO2012/1-1

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2017-10-11
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description