6T1M

Crystal structure of MLLT1 (ENL) YEATS domain in complexed with benzimidazole-amide derivative 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Insights into Interaction Mechanisms of Alternative Piperazine-urea YEATS Domain Binders in MLLT1.

Ni, X.Heidenreich, D.Christott, T.Bennett, J.Moustakim, M.Brennan, P.E.Fedorov, O.Knapp, S.Chaikuad, A.

(2019) Acs Med.Chem.Lett. 10: 1661-1666

  • DOI: 10.1021/acsmedchemlett.9b00460
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • YEATS-domain-containing MLLT1 is an acetyl/acyl-lysine reader domain, which is structurally distinct from well-studied bromodomains and has been strongly associated in development of cancer. Here, we characterized piperazine-urea derivatives as an ac ...

    YEATS-domain-containing MLLT1 is an acetyl/acyl-lysine reader domain, which is structurally distinct from well-studied bromodomains and has been strongly associated in development of cancer. Here, we characterized piperazine-urea derivatives as an acetyl/acyl-lysine mimetic moiety for MLLT1. Crystal structures revealed distinct interaction mechanisms of this chemotype compared to the recently described benzimidazole-amide based inhibitors, exploiting different binding pockets within the protein. Thus, the piperazine-urea scaffold offers an alternative strategy for targeting the YEATS domain family.


    Organizational Affiliation

    Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany.,Target Discovery Institute and Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K.,Structural Genomics Consortium, BMLS, Goethe-University Frankfurt, 60438 Frankfurt, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein ENL
A
154Homo sapiensMutation(s): 0 
Gene Names: MLLT1 (ENL, LTG19, YEATS1)
Find proteins for Q03111 (Homo sapiens)
Go to Gene View: MLLT1
Go to UniProtKB:  Q03111
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
M8K
Query on M8K

Download SDF File 
Download CCD File 
A
4-cyano-~{N}-[2-(piperidin-1-ylmethyl)-1~{H}-benzimidazol-5-yl]benzamide
C21 H21 N5 O
PYUJNKLBJTZGDT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.215 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 49.069α = 90.00
b = 49.069β = 90.00
c = 129.992γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2020-01-29
    Type: Database references