Macromolecule Content

Total Structure Weight: 105141.02
Atom Count: 7032
Residue Count: 854
Unique protein chains: 1

5LPK

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

DOI: 10.2210/pdb5LPK/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)

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

Experimental Data Snapshot

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

wwPDB Validation3D 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

PubMed: 28766825 Search on PubMed
DOI: 10.1002/anie.201705516
Primary Citation of Related Structures:
5NU5, 5NU3, 5NRW, 5LPM, 5LPL, 5LPJ

PubMed Abstract:

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
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
Find proteins for Q09472 (Homo sapiens) Go to Gene View: EP300 Go to UniProtKB: Q09472
Protein Feature View Full Protein Feature View for Q09472

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D 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
ID	Binding Affinity (Sequence Identity %)
XDM	Kd: 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 = 133.600	α = 90.00
b = 61.040	β = 98.31
c = 135.680	γ = 90.00

Software Package:

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

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History & Funding Information

Deposition Data

Deposited Date: 2016-08-13
Released Date: 2017-08-16
Deposition Author(s): Huegle, M., Wohlwend, D.

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
Type: Database references

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.