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

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
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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: 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.

Organizational Affiliation

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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase p300	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q09472
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XDM Query on XDM Download Ideal Coordinates CCD File SDF format, chain IA [auth F] SDF format, chain AA [auth D] SDF format, chain EA [auth E] SDF format, chain FA [auth E] SDF format, chain H [auth A] SDF format, chain P [auth B] SDF format, chain X [auth C] MOL2 format, chain IA [auth F] MOL2 format, chain AA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain X [auth C] mmCIF format, chain IA [auth F] mmCIF format, chain AA [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain X [auth C]	AA [auth D] EA [auth E] FA [auth E] H [auth A] IA [auth F] 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		Interactions Focus chain AA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain H [auth A] Focus chain IA [auth F] Focus chain P [auth B] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain H [auth A] Focus chain IA [auth F] Focus chain P [auth B] Focus chain X [auth C]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain W [auth B] MOL2 format, chain W [auth B] mmCIF format, chain W [auth B]	W [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain W [auth B] Interactions & Density Focus chain W [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain GA [auth E] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth F] SDF format, chain Y [auth C] MOL2 format, chain GA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain Y [auth C] mmCIF format, chain GA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain Y [auth C]	GA [auth E], I [auth A], J [auth A], JA [auth F], Y [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain GA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth F] Focus chain Y [auth C] Interactions & Density Focus chain GA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth F] Focus chain Y [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain HA [auth E] SDF format, chain K [auth A] SDF format, chain KA [auth F] SDF format, chain L [auth A] SDF format, chain LA [auth F] SDF format, chain M [auth A] SDF format, chain MA [auth G] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain Z [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth G] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain Z [auth C]	BA [auth D] CA [auth D] DA [auth D] HA [auth E] K [auth A] 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		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain HA [auth E] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth G] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain Z [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain HA [auth E] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth G] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain Z [auth C]

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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

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 (Full details and data files)

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