6UD2

co-crystal structure of compound 1 bound to human Mcl-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery and in Vivo Evaluation of Macrocyclic Mcl-1 Inhibitors Featuring an alpha-Hydroxy Phenylacetic Acid Pharmacophore or Bioisostere.

Rescourio, G.Gonzalez, A.Z.Jabri, S.Belmontes, B.Moody, G.Whittington, D.Huang, X.Caenepeel, S.Cardozo, M.Cheng, A.C.Chow, D.Dou, H.Jones, A.Kelly, R.C.Li, Y.Lizarzaburu, M.Lo, M.C.Mallari, R.Meleza, C.Rew, Y.Simonovich, S.Sun, D.Turcotte, S.Yan, X.Wong, S.G.Yanez, E.Zancanella, M.Houze, J.Medina, J.C.Hughes, P.E.Brown, S.P.

(2019) J Med Chem 62: 10258-10271

  • DOI: 10.1021/acs.jmedchem.9b01310
  • Primary Citation of Related Structures:  
    6UD2, 6UDI, 6UDT, 6UDU, 6UDV, 6UDX, 6UDY

  • PubMed Abstract: 
  • Overexpression of the antiapoptotic protein Mcl-1 provides a survival advantage to some cancer cells, making inhibition of this protein an attractive therapeutic target for the treatment of certain types of tumors. Herein, we report our efforts toward the identification of a novel series of macrocyclic Mcl-1 inhibitors featuring an α-hydroxy phenylacetic acid pharmacophore or bioisostere ...

    Overexpression of the antiapoptotic protein Mcl-1 provides a survival advantage to some cancer cells, making inhibition of this protein an attractive therapeutic target for the treatment of certain types of tumors. Herein, we report our efforts toward the identification of a novel series of macrocyclic Mcl-1 inhibitors featuring an α-hydroxy phenylacetic acid pharmacophore or bioisostere. This work led to the discovery of 1 , a potent Mcl-1 inhibitor (IC 50 = 19 nM in an OPM-2 cell viability assay) with good pharmacokinetic properties and excellent in vivo efficacy in an OPM-2 multiple myeloma xenograft model.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, Cambridge, Massachusetts.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Induced myeloid leukemia cell differentiation protein Mcl-1A157Homo sapiensMutation(s): 0 
Gene Names: MCL1BCL2L3
UniProt & NIH Common Fund Data Resources
Find proteins for Q07820 (Homo sapiens)
Explore Q07820 
Go to UniProtKB:  Q07820
PHAROS:  Q07820
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Q4D (Subject of Investigation/LOI)
Query on Q4D

Download Ideal Coordinates CCD File 
B [auth A](4S,7aR,9aR,10S,11E,18R)-6'-chloro-10-[2-(3,3-difluoroazetidin-1-yl)ethoxy]-N-(dimethylsulfamoyl)-18-hydroxy-15-methyl-16-oxo-3',4',7,7a,8,9,9a,10,13,14,15,16,17,18-tetradecahydro-2'H,3H,5H-spiro[1,19-(ethanediylidene)cyclobuta[n][1,4]oxazepino[4,3-a][1,8]diazacyclohexadecine-4,1'-naphthalene]-18-carboxamide
C40 H52 Cl F2 N5 O7 S
OCZBGAPIVMKKDK-HBUYLHAMSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
Q4D Binding MOAD:  6UD2 IC50: 0.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.028α = 90
b = 89.768β = 90
c = 84.855γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Database references