6J3P

Crystal structure of the human GCN5 bromodomain in complex with compound (R,R)-36n


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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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:  
    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) ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone acetyltransferase KAT2AA, B135Homo sapiensMutation(s): 0 
Gene Names: KAT2AGCN5GCN5L2
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92830 (Homo sapiens)
Explore Q92830 
Go to UniProtKB:  Q92830
PHAROS:  Q92830
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92830
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B8O
Query on B8O

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2-{[(3R,5R)-5-(2,3-dihydro-1,4-benzodioxin-6-yl)-1-methylpiperidin-3-yl]amino}-3-methyl-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one
C21 H25 N5 O3
PUFPGLSWMMJNSE-LSDHHAIUSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
B8O Binding MOAD:  6J3P Kd: 105 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.572α = 90
b = 73.092β = 90
c = 76.222γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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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 1.1: 2019-05-22
    Changes: Data collection, Database references