9L6M | pdb_00009l6m

Crystal Structure of BRD2 BD1 domain in complex with small molecule inhibitor Isoxazole azepine compound.

• PDB DOI: https://doi.org/10.2210/pdb9L6M/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia phage EcSzw-2
• Mutation(s): No 


• Deposited: 2024-12-24 Released: 2025-12-24 
• Deposition Author(s): Jwala, N., Vijayshankar, N., Thomas, A., NarasimhaRao, K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.248 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of BRD2 BD1 domain in complex with small molecule inhibitor CPI-0610 Pelabresib.

Jwala, N., NarasimhaRao, K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.32 kDa 
• Atom Count: 2,856 
• Modeled Residue Count: 322 
• Deposited Residue Count: 465 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 2	A, B, C	155	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1XB (Subject of Investigation/LOI)	D [auth A], E [auth B], F [auth C]	2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-[1,2]oxazolo[5,4-c]thieno[2,3-e]azepin-6-yl]acetamide C20 H18 Cl N3 O2 S DRSQZZRFHBWKKZ-AWEZNQCLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.248 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.633	α = 90
b = 56.138	β = 94.22
c = 68.118	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystalClear	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Jwala, N., Vijayshankar, N., Thomas, A., NarasimhaRao, K.

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Funding Organization	Location	Grant Number
Not funded	India	--

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release