5LOF

Crystal structure of the MBP-MCL1 complex with highly selective and potent inhibitor of MCL1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

The MCL1 inhibitor S63845 is tolerable and effective in diverse cancer models.

Kotschy, A.Szlavik, Z.Murray, J.Davidson, J.Maragno, A.L.Le Toumelin-Braizat, G.Chanrion, M.Kelly, G.L.Gong, J.N.Moujalled, D.M.Bruno, A.Csekei, M.Paczal, A.Szabo, Z.B.Sipos, S.Radics, G.Proszenyak, A.Balint, B.Ondi, L.Blasko, G.Robertson, A.Surgenor, A.Dokurno, P.Chen, I.Matassova, N.Smith, J.Pedder, C.Graham, C.Studeny, A.Lysiak-Auvity, G.Girard, A.M.Grave, F.Segal, D.Riffkin, C.D.Pomilio, G.Galbraith, L.C.Aubrey, B.J.Brennan, M.S.Herold, M.J.Chang, C.Guasconi, G.Cauquil, N.Melchiore, F.Guigal-Stephan, N.Lockhart, B.Colland, F.Hickman, J.A.Roberts, A.W.Huang, D.C.Wei, A.H.Strasser, A.Lessene, G.Geneste, O.

(2016) Nature 538: 477-482

  • DOI: https://doi.org/10.1038/nature19830
  • Primary Citation of Related Structures:  
    5LOF

  • PubMed Abstract: 

    Avoidance of apoptosis is critical for the development and sustained growth of tumours. The pro-survival protein myeloid cell leukemia 1 (MCL1) is overexpressed in many cancers, but the development of small molecules targeting this protein that are amenable for clinical testing has been challenging. Here we describe S63845, a small molecule that specifically binds with high affinity to the BH3-binding groove of MCL1. Our mechanistic studies demonstrate that S63845 potently kills MCL1-dependent cancer cells, including multiple myeloma, leukaemia and lymphoma cells, by activating the BAX/BAK-dependent mitochondrial apoptotic pathway. In vivo, S63845 shows potent anti-tumour activity with an acceptable safety margin as a single agent in several cancers. Moreover, MCL1 inhibition, either alone or in combination with other anti-cancer drugs, proved effective against several solid cancer-derived cell lines. These results point towards MCL1 as a target for the treatment of a wide range of tumours.


  • Organizational Affiliation

    Servier Research Institute of Medicinal Chemistry, Budapest 1031, Hungary.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose-binding periplasmic protein,Induced myeloid leukemia cell differentiation protein Mcl-1518Escherichia coli O157:H7Homo sapiens
This entity is chimeric
Mutation(s): 6 
Gene Names: malEZ5632ECs5017MCL1BCL2L3
UniProt & NIH Common Fund Data Resources
Find proteins for Q07820 (Homo sapiens)
Explore Q07820 
Go to UniProtKB:  Q07820
PHAROS:  Q07820
GTEx:  ENSG00000143384 
Find proteins for P0AEY0 (Escherichia coli O157:H7)
Explore P0AEY0 
Go to UniProtKB:  P0AEY0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0AEY0Q07820
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
70R
Query on 70R

Download Ideal Coordinates CCD File 
C [auth A](2~{R})-2-[5-[3-chloranyl-2-methyl-4-[2-(4-methylpiperazin-1-yl)ethoxy]phenyl]-6-(5-fluoranylfuran-2-yl)thieno[2,3-d]pyrimidin-4-yl]oxy-3-[2-[[2-[2,2,2-tris(fluoranyl)ethyl]pyrazol-3-yl]methoxy]phenyl]propanoic acid
C39 H37 Cl F4 N6 O6 S
ZFBHXVOCZBPADE-SSEXGKCCSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
70R Binding MOAD:  5LOF Kd: 0.19 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.4α = 90
b = 136.76β = 90
c = 38.33γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-02
    Changes: Database references
  • Version 1.2: 2016-11-09
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary