8DKB

Crystal Structure of human YEATS4 in complex with Pfizer small molecule compound 3b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of High-Affinity Small-Molecule Binders of the Epigenetic Reader YEATS4.

Londregan, A.T.Aitmakhanova, K.Bennett, J.Byrnes, L.J.Canterbury, D.P.Cheng, X.Christott, T.Clemens, J.Coffey, S.B.Dias, J.M.Dowling, M.S.Farnie, G.Fedorov, O.Fennell, K.F.Gamble, V.Gileadi, C.Giroud, C.Harris, M.R.Hollingshead, B.D.Huber, K.Korczynska, M.Lapham, K.Loria, P.M.Narayanan, A.Owen, D.R.Raux, B.Sahasrabudhe, P.V.Ruggeri, R.B.Saez, L.D.Stock, I.A.Thuma, B.A.Tsai, A.Varghese, A.E.

(2023) J Med Chem 66: 460-472

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01421
  • Primary Citation of Related Structures:  
    8DKB

  • PubMed Abstract: 

    A series of small-molecule YEATS4 binders have been discovered as part of an ongoing research effort to generate high-quality probe molecules for emerging and/or challenging epigenetic targets. Analogues such as 4d and 4e demonstrate excellent potency and selectivity for YEATS4 binding versus YEATS1,2,3 and exhibit good physical properties and in vitro safety profiles. A new X-ray crystal structure confirms direct binding of this chemical series to YEATS4 at the lysine acetylation recognition site of the YEATS domain. Multiple analogues engage YEATS4 with nanomolar potency in a whole-cell nanoluciferase bioluminescent resonance energy transfer assay. Rodent pharmacokinetic studies demonstrate the competency of several analogues as in vivo-capable binders.


  • Organizational Affiliation

    Pfizer Medicine Design, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
YEATS domain-containing protein 4
A, B, C, D, E
A, B, C, D, E, F, G, H
155Homo sapiensMutation(s): 0 
Gene Names: YEATS4GAS41
UniProt & NIH Common Fund Data Resources
Find proteins for O95619 (Homo sapiens)
Explore O95619 
Go to UniProtKB:  O95619
PHAROS:  O95619
GTEx:  ENSG00000127337 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95619
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.6α = 90
b = 109.3β = 95.68
c = 103.83γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2023-01-25
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description