6J3O | pdb_00006j3o

Crystal structure of the human PCAF bromodomain in complex with compound 12

• PDB DOI: https://doi.org/10.2210/pdb6J3O/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-05 Released: 2019-05-01 
• Deposition Author(s): Huang, L.Y., Li, H., Li, L.L., Niu, L., Seupel, R., Wu, C.Y., Li, G.B., Yu, Y.M., Brennan, P.E., Yang, S.Y.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.257 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Discovery of Pyrrolo[3,2- d]pyrimidin-4-one Derivatives as a New Class of Potent and Cell-Active Inhibitors of P300/CBP-Associated Factor Bromodomain.

Huang, L., Li, H., Li, L., Niu, L., Seupel, R., Wu, C., Cheng, W., Chen, C., Ding, B., Brennan, P.E., Yang, S.

(2019) J Med Chem 62: 4526-4542

• PubMed: 30998845 
• DOI: https://doi.org/10.1021/acs.jmedchem.9b00096
• Primary Citation Related Structures: 
  6J3O, 6J3P


• PubMed Abstract: 
  

  Herein, we report the discovery of a series of new P300/CBP-associated factor (PCAF) bromodomain (BRD) inhibitors, which were obtained through a hit discovery process and subsequent structure-based optimization and structure-activity relationship analyses toward a retrieved hit compound (12). Among these inhibitors, ( R, R)-36n is the most potent one with an IC ₅₀ of 7 nM in homogeneous time-resolved fluorescence assay and a K _D of 78 nM in isothermal titration calorimetry assay. This compound also exhibited activity against GCN5 and FALZ, but weak or no activity against other 29 BRD proteins and 422 kinases, indicating considerable selectivity. X-ray cocrystal structure analysis revealed the molecular interaction mode and the precise stereochemistry required for bioactivity. Cellular activity, preliminary RNA-seq analysis, and pharmacokinetic properties were also examined for this compound. Collectively, this study provides a versatile tool molecule to explore molecular mechanisms of PCAF BRD regulation and also offers a new lead compound for drug discovery targeting PCAF.

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Organizational Affiliation: 
• State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University , Chengdu 610041 , P. R. China.
Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy , Sichuan University , Sichuan 610041 , P. R. China.
Structural Genomics Consortium , University of Oxford , Old Road Campus Research Building, Roosevelt Drive , Oxford OX3 7DQ , U.K.
Target Discovery Institute , University of Oxford , NDM Research Building, Roosevelt Drive , Oxford OX3 7FZ , U.K.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.81 kDa 
• Atom Count: 1,843 
• Modeled Residue Count: 211 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase KAT2B	A, B	140	Homo sapiens	Mutation(s): 0  Gene Names: KAT2B, PCAF EC: 2.3.1.48 (PDB Primary Data), 2.3.1.57 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92831 (Homo sapiens) Explore Q92831  Go to UniProtKB:  Q92831
PHAROS:  Q92831 GTEx:  ENSG00000114166

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B4L	C [auth A], D [auth B]	3-methyl-2-[[(3~{R})-1-methylpiperidin-3-yl]amino]-5~{H}-pyrrolo[3,2-d]pyrimidin-4-one C13 H19 N5 O DIBDHOFCFXCFCB-SECBINFHSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
B4L	BindingDB:  6J3O	Kd: 2400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.257 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.52	α = 90
b = 101.52	β = 90
c = 99.68	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-05-01 
Deposition Author(s): Huang, L.Y., Li, H., Li, L.L., Niu, L., Seupel, R., Wu, C.Y., Li, G.B., Yu, Y.M., Brennan, P.E., Yang, S.Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81473140, 81573349, 81773633, and 21772130

Revision History  

• Version 1.0: 2019-05-01
  Type: Initial release
  
• Version 2.0: 2019-05-22
  Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description