6HT0

Crystal structure of MLLT1 (ENL) YEATS domain in complexed with compound 94


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.230 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GQ8Click on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Discovery of an MLLT1/3 YEATS Domain Chemical Probe.

Moustakim, M.Christott, T.Monteiro, O.P.Bennett, J.Giroud, C.Ward, J.Rogers, C.M.Smith, P.Panagakou, I.Diaz-Saez, L.Felce, S.L.Gamble, V.Gileadi, C.Halidi, N.Heidenreich, D.Chaikuad, A.Knapp, S.Huber, K.V.M.Farnie, G.Heer, J.Manevski, N.Poda, G.Al-Awar, R.Dixon, D.J.Brennan, P.E.Fedorov, O.

(2018) Angew Chem Int Ed Engl 57: 16302-16307

  • DOI: https://doi.org/10.1002/anie.201810617
  • Primary Citation of Related Structures:  
    6HT0, 6HT1

  • PubMed Abstract: 

    YEATS domain (YD) containing proteins are an emerging class of epigenetic targets in drug discovery. Dysregulation of these modified lysine-binding proteins has been linked to the onset and progression of cancers. We herein report the discovery and characterisation of the first small-molecule chemical probe, SGC-iMLLT, for the YD of MLLT1 (ENL/YEATS1) and MLLT3 (AF9/YEATS3). SGC-iMLLT is a potent and selective inhibitor of MLLT1/3-histone interactions. Excellent selectivity over other human YD proteins (YEATS2/4) and bromodomains was observed. Furthermore, our probe displays cellular target engagement of MLLT1 and MLLT3. The first small-molecule X-ray co-crystal structures with the MLLT1 YD are also reported. This first-in-class probe molecule can be used to understand MLLT1/3-associated biology and the therapeutic potential of small-molecule YD inhibitors.


  • Organizational Affiliation

    Structural Genomics Consortium & Target Discovery Institute, University of Oxford, NDMRB, Old Road Campus, Oxford, OX3 7DQ &, OX3 7FZ, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein ENL155Homo sapiensMutation(s): 0 
Gene Names: MLLT1ENLLTG19YEATS1
UniProt & NIH Common Fund Data Resources
Find proteins for Q03111 (Homo sapiens)
Explore Q03111 
Go to UniProtKB:  Q03111
PHAROS:  Q03111
GTEx:  ENSG00000130382 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03111
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GQ8
Query on GQ8

Download Ideal Coordinates CCD File 
K [auth A]1-cyclopropyl-~{N}-[2-[[(2~{S})-2-methylpyrrolidin-1-yl]methyl]-3~{H}-benzimidazol-5-yl]indazole-5-carboxamide
C24 H26 N6 O
FTNYJPRHIRILOI-HNNXBMFYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.230 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.754α = 90
b = 48.754β = 90
c = 132.858γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GQ8Click on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2018-12-12
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description