7B10

Crystal structure of MLLT1 YEATS domain T1 mutant in complex with benzimidazole-amide based compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structure and Inhibitor Binding Characterization of Oncogenic MLLT1 Mutants.

Ni, X.Londregan, A.T.Owen, D.R.Knapp, S.Chaikuad, A.

(2021) ACS Chem Biol 16: 571-578

  • DOI: https://doi.org/10.1021/acschembio.0c00960
  • Primary Citation of Related Structures:  
    7B0T, 7B10

  • PubMed Abstract: 

    Dysfunction of YEATS-domain-containing MLLT1, an acetyl/acyl-lysine dependent epigenetic reader domain, has been implicated in the development of aggressive cancers. Mutations in the YEATS domain have been recently reported as a cause of MLLT1 aberrant reader function. However, the structural basis for the reported alterations in affinity for acetylated/acylated histone has remained elusive. Here, we report the crystal structures of both insertion and substitution mutants present in cancer, revealing significant conformational changes of the YEATS-domain loop 8. Structural comparison demonstrates that not only did such alteration alter the binding interface for acetylated/acylated histones, but the sequence alterations in the loop in T1 mutant may enable dimeric assembly consistent with inducing self-association behavior. Nevertheless, we show that also the MLLT1 mutants can be targeted by developed acetyllysine mimetic inhibitors with affinities similarly to wild-type. Our report provides a structural basis for the altered behaviors and a potential strategy for targeting oncogenic MLLT1 mutants.


  • Organizational Affiliation

    Structural Genomics Consortium and Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein ENL157Homo 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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GKT (Subject of Investigation/LOI)
Query on GKT

Download Ideal Coordinates CCD File 
B [auth A]3-iodanyl-4-methyl-~{N}-[2-(piperidin-1-ylmethyl)-3~{H}-benzimidazol-5-yl]benzamide
C21 H23 I N4 O
VMKBJIIRNPWSSI-UHFFFAOYSA-N
IOD
Query on IOD

Download Ideal Coordinates CCD File 
C [auth A]IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO
Query on EDO

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.111α = 90
b = 39.357β = 125.58
c = 53.111γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release
  • Version 1.1: 2021-04-14
    Changes: Database references
  • Version 1.2: 2021-04-28
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Database references, Refinement description