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 

Starting Model: experimental
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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 BindingDB:  5LOF Ki: min: 0.19, max: 1.2 (nM) from 2 assay(s)
Kd: 0.19 (nM) from 1 assay(s)
IC50: 1.00e+6 (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