X-ray co-crystal structure of compound 5 with Mcl-1

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.250 

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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-1
A, B
157Homo 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
GTEx:  ENSG00000143384 
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
Q54 (Subject of Investigation/LOI)
Query on Q54

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(3S)-6'-chloro-5-(cyclobutylmethyl)-3',4,4',5-tetrahydro-2H,2'H-spiro[1,5-benzoxazepine-3,1'-naphthalene]-7-carboxylic acid
C24 H26 Cl N O3
Binding Affinity Annotations 
IDSourceBinding Affinity
Q54 Binding MOAD:  6UDY IC50: 27 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.250 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.271α = 90
b = 84.954β = 90
c = 90.328γ = 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

  • Released Date: 2019-12-11 
  • Deposition Author(s): Huang, X.

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Data collection, Database references