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

Experimental Data Snapshot

  • 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 

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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: https://doi.org/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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Induced myeloid leukemia cell differentiation protein Mcl-1157Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07820
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / 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
Binding Affinity Annotations 
IDSourceBinding Affinity
Q4D Binding MOAD:  6UD2 IC50: 0.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • 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
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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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