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

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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

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

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

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8M6 (Subject of Investigation/LOI)	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
EDO	C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Entry History & Funding Information

Deposition Data

• Released Date: 2022-04-20 
Deposition Author(s): Carrasco, K., Betzi, S., Morelli, X.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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