6QYP

Structure of Mcl-1 in complex with compound 13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-Guided Discovery of a Selective Mcl-1 Inhibitor with Cellular Activity.

Szlavik, Z.Ondi, L.Csekei, M.Paczal, A.Szabo, Z.B.Radics, G.Murray, J.Davidson, J.Chen, I.Davis, B.Hubbard, R.E.Pedder, C.Dokurno, P.Surgenor, A.Smith, J.Robertson, A.LeToumelin-Braizat, G.Cauquil, N.Zarka, M.Demarles, D.Perron-Sierra, F.Claperon, A.Colland, F.Geneste, O.Kotschy, A.

(2019) J.Med.Chem. 62: 6913-6924

  • DOI: 10.1021/acs.jmedchem.9b00134
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Myeloid cell leukemia 1 (Mcl-1), an antiapoptotic member of the Bcl-2 family of proteins, whose upregulation when observed in human cancers is associated with high tumor grade, poor survival, and resistance to chemotherapy, has emerged as an attracti ...

    Myeloid cell leukemia 1 (Mcl-1), an antiapoptotic member of the Bcl-2 family of proteins, whose upregulation when observed in human cancers is associated with high tumor grade, poor survival, and resistance to chemotherapy, has emerged as an attractive target for cancer therapy. Here, we report the discovery of selective small molecule inhibitors of Mcl-1 that inhibit cellular activity. Fragment screening identified thienopyrimidine amino acids as promising but nonselective hits that were optimized using nuclear magnetic resonance and X-ray-derived structural information. The introduction of hindered rotation along a biaryl axis has conferred high selectivity to the compounds, and cellular activity was brought on scale by offsetting the negative charge of the anchoring carboxylate group. The obtained compounds described here exhibit nanomolar binding affinity and mechanism-based cellular efficacy, caspase induction, and growth inhibition. These early research efforts illustrate drug discovery optimization from thienopyrimidine hits to a lead compound, the chemical series leading to the identification of our more advanced compounds S63845 and S64315.


    Organizational Affiliation

    Servier Research Institute of Medicinal Chemistry , Záhony u. 7. , H-1031 Budapest , Hungary.,Technologie Servier , 27 Rue Eugène Vignat , 45000 Orleans , France.,Institute de Recherche Servier , 125 Chemin de Ronde , 78290 Croissy-sur-Seine , France.,Vernalis (R&D) Ltd. , Granta Park , Cambridge CB21 6GB , U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Induced myeloid leukemia cell differentiation protein Mcl-1
A
170Homo sapiensMutation(s): 0 
Gene Names: MCL1 (BCL2L3)
Find proteins for Q07820 (Homo sapiens)
Go to Gene View: MCL1
Go to UniProtKB:  Q07820
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JL5
Query on JL5

Download SDF File 
Download CCD File 
A
(2~{R})-2-[5-[3-chloranyl-2-methyl-5-(4-methylpiperazin-1-yl)-4-oxidanyl-phenyl]-6-ethyl-thieno[2,3-d]pyrimidin-4-yl]oxy-3-phenyl-propanoic acid
C29 H31 Cl N4 O4 S
OZKTZQZOQQOTJP-OAQYLSRUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.198 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 40.165α = 90.00
b = 40.165β = 90.00
c = 327.800γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-08-21
    Type: Data collection, Database references
  • Version 1.2: 2019-09-18
    Type: Data collection, Refinement description