6J3O

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


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

  • DOI: 10.1021/acs.jmedchem.9b00096
  • Primary Citation of Related Structures:  
    6J3P, 6J3O

  • 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) ...

    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.


    Organizational Affiliation

    State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University , Chengdu 610041 , P. R. China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone acetyltransferase KAT2BA, B140Homo sapiensMutation(s): 0 
Gene Names: KAT2BPCAF
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B4L (Subject of Investigation/LOI)
Query on B4L

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
B4L Binding MOAD:  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 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.52α = 90
b = 101.52β = 90
c = 99.68γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81473140, 81573349, 81773633, and 21772130

Revision History  (Full details and data files)

  • 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