6T1M

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

• PDB DOI: https://doi.org/10.2210/pdb6T1M/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-10-04 Released: 2019-11-06 
• Deposition Author(s): Chaikuad, A., Heidenreich, D., Moustakim, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Fedorov, O., Brennan, P.E., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.275 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 

Starting Model: experimental

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

• PubMed: 31857843 
• DOI: https://doi.org/10.1021/acsmedchemlett.9b00460
• Primary Citation of Related Structures:  
  6T1I, 6T1J, 6T1L, 6T1M, 6T1N, 6T1O


• 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 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.

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Organizational Affiliation: 

Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.02 kDa 
• Atom Count: 1,288 
• Modelled Residue Count: 142 
• Deposited Residue Count: 154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein ENL	A	154	Homo sapiens	Mutation(s): 0  Gene Names: MLLT1, ENL, LTG19, YEATS1
UniProt & NIH Common Fund Data Resources
Find proteins for Q03111 (Homo sapiens) Explore Q03111  Go to UniProtKB:  Q03111
PHAROS:  Q03111 GTEx:  ENSG00000130382

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M8K (Subject of Investigation/LOI)	B [auth A]	4-cyano-~{N}-[2-(piperidin-1-ylmethyl)-1~{H}-benzimidazol-5-yl]benzamide C21 H21 N5 O PYUJNKLBJTZGDT-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
M8K	BindingDB:  6T1M	Kd: min: 2400, max: 6100 (nM) from 2 assay(s)
		IC50: 2600 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.275 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.069	α = 90
b = 49.069	β = 90
c = 129.992	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-11-06 
Deposition Author(s): Chaikuad, A., Heidenreich, D., Moustakim, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Fedorov, O., Brennan, P.E., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2019-11-06
  Type: Initial release
  
• Version 1.1: 2020-01-29
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description