6WZW

Ash1L SET domain in complex with AS-85


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of first-in-class inhibitors of ASH1L histone methyltransferase with anti-leukemic activity.

Rogawski, D.S.Deng, J.Li, H.Miao, H.Borkin, D.Purohit, T.Song, J.Chase, J.Li, S.Ndoj, J.Klossowski, S.Kim, E.Mao, F.Zhou, B.Ropa, J.Krotoska, M.Z.Jin, Z.Ernst, P.Feng, X.Huang, G.Nishioka, K.Kelly, S.He, M.Wen, B.Sun, D.Muntean, A.Dou, Y.Maillard, I.Cierpicki, T.Grembecka, J.

(2021) Nat Commun 12: 2792-2792

  • DOI: https://doi.org/10.1038/s41467-021-23152-6
  • Primary Citation of Related Structures:  
    6WZW, 6X0P

  • PubMed Abstract: 

    ASH1L histone methyltransferase plays a crucial role in the pathogenesis of different diseases, including acute leukemia. While ASH1L represents an attractive drug target, developing ASH1L inhibitors is challenging, as the catalytic SET domain adapts an inactive conformation with autoinhibitory loop blocking the access to the active site. Here, by applying fragment-based screening followed by medicinal chemistry and a structure-based design, we developed first-in-class small molecule inhibitors of the ASH1L SET domain. The crystal structures of ASH1L-inhibitor complexes reveal compound binding to the autoinhibitory loop region in the SET domain. When tested in MLL leukemia models, our lead compound, AS-99, blocks cell proliferation, induces apoptosis and differentiation, downregulates MLL fusion target genes, and reduces the leukemia burden in vivo. This work validates the ASH1L SET domain as a druggable target and provides a chemical probe to further study the biological functions of ASH1L as well as to develop therapeutic agents.


  • Organizational Affiliation

    Department of Pathology, University of Michigan, Ann Arbor, MI, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase ASH1L226Homo sapiensMutation(s): 0 
Gene Names: ASH1LKIAA1420KMT2H
EC: 2.1.1 (PDB Primary Data), 2.1.1.359 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NR48 (Homo sapiens)
Explore Q9NR48 
Go to UniProtKB:  Q9NR48
PHAROS:  Q9NR48
GTEx:  ENSG00000116539 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NR48
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UG7 (Subject of Investigation/LOI)
Query on UG7

Download Ideal Coordinates CCD File 
G [auth A]N-{[3-(3-carbamothioylphenyl)-1-{1-[(trifluoromethyl)sulfonyl]piperidin-4-yl}-1H-indol-6-yl]methyl}azetidine-3-carboxamide
C26 H28 F3 N5 O3 S2
WDQKQCWRQIVDBA-UHFFFAOYSA-N
SAM
Query on SAM

Download Ideal Coordinates CCD File 
C [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
B [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.277α = 90
b = 31.998β = 102.341
c = 91.16γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA244254

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2021-05-26
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description