7VD4

Crystal structure of BPTF-BRD with ligand TP248 bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of a highly potent CECR2 bromodomain inhibitor with 7H-pyrrolo[2,3-d] pyrimidine scaffold.

Lu, H.Lu, T.Zu, S.Duan, Z.Guang, Y.Li, Q.Ma, J.Chen, D.Li, B.Lu, W.Jiang, H.Luo, C.Ye, D.Chen, K.Lin, H.

(2022) Bioorg Chem 123: 105768-105768

  • DOI: https://doi.org/10.1016/j.bioorg.2022.105768
  • Primary Citation of Related Structures:  
    7VD4

  • PubMed Abstract: 

    Cat eye syndrome chromosome region candidate 2 (CECR2) bromodomain is a module of CECR2-containing remodeling factor (CERF), which is a chromatin remodeling complex correlating with transcriptional control and adjustment of chromatin architecture. Potent chemical probes would be beneficial to gain insights into the biochemical and pharmacological functions of CECR2 BRD. Herein, we report the discovery of a series of CECR2 BRD inhibitors with 7H-pyrrolo[2,3-d] pyrimidine scaffold based on molecular docking model of TP-248 and CECR2 BRD. The most potent inhibitor of this series, DC-CBi-22 with IC 50 of 8.0 ± 1.4 nM against CECR2 BRD and selectivity over BPTF BRD up to 24.9-fold. The SARs were detailed according to molecular docking. DC-CBi-22 would serve as a useful chemical probe for the study of CECR2.


  • Organizational Affiliation

    School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleosome-remodeling factor subunit BPTF114Homo sapiensMutation(s): 0 
Gene Names: BPTF
UniProt & NIH Common Fund Data Resources
Find proteins for Q12830 (Homo sapiens)
Explore Q12830 
Go to UniProtKB:  Q12830
PHAROS:  Q12830
GTEx:  ENSG00000171634 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12830
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6FI (Subject of Investigation/LOI)
Query on 6FI

Download Ideal Coordinates CCD File 
B [auth A]6-[4-[3-(dimethylamino)propoxy]phenyl]-N-methyl-2-methylsulfonyl-pyrimidin-4-amine
C17 H24 N4 O3 S
YBXAQIKRNSWPHA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.923α = 90
b = 27.219β = 98.031
c = 38.727γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
Aimlessdata scaling
PHASESphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-14
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description