7C9N

Crystal structure of SETDB1 tudor domain in complexed with Compound 1.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.196 

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This is version 1.2 of the entry. See complete history


Literature

Structure-Guided Discovery of a Potent and Selective Cell-Active Inhibitor of SETDB1 Tudor Domain.

Guo, Y.Mao, X.Xiong, L.Xia, A.You, J.Lin, G.Wu, C.Huang, L.Wang, Y.Yang, S.

(2021) Angew Chem Int Ed Engl 60: 8760-8765

  • DOI: https://doi.org/10.1002/anie.202017200
  • Primary Citation of Related Structures:  
    7C9N, 7CAJ, 7CD9, 7CJT

  • PubMed Abstract: 

    SET domain bifurcated protein 1 (SETDB1) is a histone lysine methyltransferase that promotes the silencing of some tumour suppressor genes and is overexpressed in many cancers. SETDB1 contains a unique tandem tudor domain (TTD) that recognizes histone H3 sequences containing both methylated and acetylated lysines. Beginning with the identification of a hit compound (Cpd1), we discovered the first potent and selective small molecule SETDB1-TTD inhibitor (R,R)-59 through stepwise structure-guided optimization. (R,R)-59 showed a K D value of 0.088±0.045 μM in the ITC assay. The high potency of (R,R)-59 was well explained by the cocrystal structure of the (R,R)-59-TTD complex. (R,R)-59 is an endogenous binder competitive inhibitor. Evidence has also demonstrated its cellular target engagement. Interestingly, the enantiomer (S,S)-59 did not show activity in all the assays, highlighting the potential of (R,R)-59 as a tool compound in exploring the biological functions of SETDB1-TTD.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase SETDB1A [auth B],
B [auth A]
240Homo sapiensMutation(s): 0 
Gene Names: SETDB1ESETKIAA0067KMT1E
EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15047 (Homo sapiens)
Explore Q15047 
Go to UniProtKB:  Q15047
PHAROS:  Q15047
GTEx:  ENSG00000143379 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15047
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FN9 (Subject of Investigation/LOI)
Query on FN9

Download Ideal Coordinates CCD File 
C [auth B],
D [auth A]
3,5-dimethyl-2-[[(3R,5R)-1-methyl-5-phenyl-piperidin-3-yl]amino]pyrrolo[3,2-d]pyrimidin-4-one
C20 H25 N5 O
FAOILJOQEQTGLJ-JKSUJKDBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.715α = 90
b = 86.67β = 90
c = 102.66γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
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 China (NSFC)China81930125

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2021-04-14
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description