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 

wwPDB Validation   3D Report Full Report


This is version 2.0 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: 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 ...

    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

    Institut de Recherches Servier Oncology R&D Unit, Croissy Sur Seine 78290, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Maltose-binding periplasmic protein,Induced myeloid leukemia cell differentiation protein Mcl-1A518Escherichia coli O157:H7Homo sapiens
This entity is chimeric
Mutation(s): 6 
Gene Names: malEZ5632ECs5017MCL1BCL2L3
Find proteins for Q07820 (Homo sapiens)
Explore Q07820 
Go to UniProtKB:  Q07820
NIH Common Fund Data Resources
PHAROS:  Q07820
Find proteins for P0AEY0 (Escherichia coli O157:H7)
Explore P0AEY0 
Go to UniProtKB:  P0AEY0
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseB2 N/A Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / 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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
70RKd:  0.1899999976158142   nM  Binding MOAD
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
Balpha-maltoseOligosaccharide /  Nutrient

--

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

View Full Validation Report



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