7Q5O

Bromodomain-containing 2 BD2 in complex with the inhibitor CRCM5484

PDB DOI: https://doi.org/10.2210/pdb7Q5O/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2021-11-04 Released: 2022-04-20
Deposition Author(s): Carrasco, K., Betzi, S., Morelli, X.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free: 0.246
R-Value Work: 0.216
R-Value Observed: 0.218

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

CRCM5484: A BET-BDII Selective Compound with Differential Anti-leukemic Drug Modulation

Carrasco, K., Montersino, C., Derviaux, C., Saez-Ayala, M., Hoffer, L., Restouin, A., Castellano, R., Casassa, J., Roche, P., Pasquier, E., Combes, S., Morelli, X., Collette, Y., Betzi, S.

(2022) J Med Chem 65: 5660-5674

DOI: https://doi.org/10.1021/acs.jmedchem.1c02168

Macromolecule Content

Total Structure Weight: 13.62 kDa
Atom Count: 1,146
Modelled Residue Count: 110
Deposited Residue Count: 110
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 2	A	110	Homo sapiens	Mutation(s): 0 Gene Names: BRD2, KIAA9001, RING3
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens) Explore P25440 Go to UniProtKB: P25440
PHAROS: P25440 GTEx: ENSG00000204256
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25440
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8M6 (Subject of Investigation/LOI) Query on 8M6 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-[[11-ethanoyl-4-(furan-2-ylmethyl)-3-oxidanylidene-8-thia-4,6,11-triazatricyclo[7.4.0.0^{2,7}]trideca-1(9),2(7),5-trien-5-yl]sulfanyl]-~{N}-(2-methylpyridin-3-yl)ethanamide C₂₄ H₂₃ N₅ O₄ S₂ PQYXGDZAWKQEEM-UHFFFAOYSA-N		Interactions Focus chain B [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
8M6	BindingDB: 7Q5O	IC50: min: 71, max: 4700 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free: 0.246
R-Value Work: 0.216
R-Value Observed: 0.218
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.43	α = 90
b = 72.494	β = 90
c = 32.041	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-04-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-04-20
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.