9F9A

Crystal structure of MUS81-EME1 bound by compound 12.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Fragment-Based Discovery of Novel MUS81 Inhibitors.

Collie, G.W.Borjesson, U.Chen, Y.Dong, Z.Di Fruscia, P.Gohlke, A.Hoyle, A.Hunt, T.A.Jesani, M.H.Luo, H.Luptak, J.Milbradt, A.G.Narasimhan, P.Packer, M.Patel, S.Qiao, J.Storer, R.I.Stubbs, C.J.Tart, J.Truman, C.Wang, A.T.Wheeler, M.G.Winter-Holt, J.

(2024) ACS Med Chem Lett 15: 1151-1158

  • DOI: https://doi.org/10.1021/acsmedchemlett.3c00453
  • Primary Citation of Related Structures:  
    9F98, 9F99, 9F9A, 9F9K, 9F9L, 9F9M

  • PubMed Abstract: 

    MUS81 is a structure-selective endonuclease that cleaves various branched DNA structures arising from natural physiological processes such as homologous recombination and mitosis. Due to this, MUS81 is able to relieve replication stress, and its function has been reported to be critical to the survival of many cancers, particularly those with dysfunctional DNA-repair machinery. There is therefore interest in MUS81 as a cancer drug target, yet there are currently few small molecule inhibitors of this enzyme reported, and no liganded crystal structures are available to guide hit optimization. Here we report the fragment-based discovery of novel small molecule MUS81 inhibitors with sub-μM biochemical activity. These inhibitors were used to develop a novel crystal system, providing the first structural insight into the inhibition of MUS81 with small molecules.


  • Organizational Affiliation

    R&D, AstraZeneca, Cambridge CB2 0AA, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Crossover junction endonuclease MUS81
A, C, E, G
308Homo sapiensMutation(s): 0 
Gene Names: MUS81
EC: 3.1.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q96NY9 (Homo sapiens)
Explore Q96NY9 
Go to UniProtKB:  Q96NY9
PHAROS:  Q96NY9
GTEx:  ENSG00000172732 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96NY9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Crossover junction endonuclease EME1
B, D, F, H
326Homo sapiensMutation(s): 0 
Gene Names: EME1MMS4
EC: 3.1.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q96AY2 (Homo sapiens)
Explore Q96AY2 
Go to UniProtKB:  Q96AY2
PHAROS:  Q96AY2
GTEx:  ENSG00000154920 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96AY2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IA6 (Subject of Investigation/LOI)
Query on A1IA6

Download Ideal Coordinates CCD File 
I [auth A],
L [auth C],
O [auth E],
R [auth G]
2-naphthalen-2-yl-5-oxidanyl-6-oxidanylidene-1H-pyrimidine-4-carboxylic acid
C15 H10 N2 O4
HQQIELXMZFSTOA-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
M [auth C]
N [auth C]
P [auth E]
J [auth A],
K [auth A],
M [auth C],
N [auth C],
P [auth E],
Q [auth E],
S [auth G],
T [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.869α = 90
b = 124.348β = 90
c = 217.571γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2024-06-19 
  • Deposition Author(s): Collie, G.W.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release
  • Version 1.1: 2024-07-31
    Changes: Database references