8FTA | pdb_00008fta

Crystal Structure of the second bromodomain of human Polybromo-1 (PB1) in complex with compound 16

• PDB DOI: https://doi.org/10.2210/pdb8FTA/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-01-11 Released: 2024-01-24 
• Deposition Author(s): Nunez, R., Smith, B.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), American Heart Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.207 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Polybromo-1 Bromodomain Inhibitor Selectivity Is Mediated by a Unique Ligand-Binding Pocket

Nunez, R., Bursch, K.L., Makowski, S.J., Xue, M., Cozzolino, K.A., Shishodia, S., Keyes, R.F., Zhu, N., Smith, B.C.

(2025) ACS Med Chem Lett 

• DOI: https://doi.org/10.1021/acsmedchemlett.5c00352

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.63 kDa 
• Atom Count: 1,122 
• Modeled Residue Count: 116 
• Deposited Residue Count: 116 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein polybromo-1	A	116	Homo sapiens	Mutation(s): 0  Gene Names: PBRM1, BAF180, PB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q86U86 (Homo sapiens) Explore Q86U86  Go to UniProtKB:  Q86U86
PHAROS:  Q86U86 GTEx:  ENSG00000163939

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y8X (Subject of Investigation/LOI)	B [auth A]	(2S)-5-chloro-2-(3-methylphenyl)-2,3-dihydroquinazolin-4(1H)-one C15 H13 Cl N2 O OBDBCXGMLSMARG-AWEZNQCLSA-N
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
Y8X	BindingDB:  8FTA	Kd: min: 1480, max: 3900 (nM) from 3 assay(s)
		IC50: 260 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.207 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.657	α = 90
b = 49.305	β = 97.75
c = 33.544	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystalClear	data collection
PDB_EXTRACT	data extraction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-24 
Deposition Author(s): Nunez, R., Smith, B.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM128840
American Heart Association	United States	--

Revision History  

• Version 1.0: 2024-01-24
  Type: Initial release
  
• Version 1.1: 2025-10-08
  Changes: Database references, Structure summary