9PW6 | pdb_00009pw6

Myeloid cell leukemia-1 (Mcl-1) complexed with compound 8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 
    0.258 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.189 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Discovery of Macrocyclic Myeloid Cell Leukemia 1 (Mcl-1) Inhibitors that Demonstrate Potent Cellular Efficacy and In Vivo Activity in a Mouse Solid Tumor Xenograft Model.

Tarr, J.C.Jeon, K.Veerasamy, N.Aichinger, M.Salovich, J.M.Zhao, B.Sensintaffar, J.L.Arnhof, H.Wunberg, T.Sgubin, D.Arnold, A.Vekariya, R.H.Christov, P.P.Kim, K.Fuchs, J.E.Karier, P.Betzemeier, B.Van Meveren, M.Miriyala, N.Olejniczak, E.T.Engelhardt, H.Lee, T.McConnell, D.Fesik, S.W.

(2025) J Med Chem 68: 18553-18578

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01376
  • Primary Citation of Related Structures:  
    9PW6, 9PW7

  • PubMed Abstract: 

    The B cell lymphoma 2 (Bcl-2) family of proteins are key regulators of intrinsic apoptosis. The antiapoptotic protein myeloid cell leukemia 1 (Mcl-1), which is associated with high tumor grade, poor survival, and resistance to treatment, has emerged as a promising candidate for treating hematological and solid cancers. Herein, we report the structure-guided design of small molecule macrocyclic Mcl-1 inhibitors based on the ( R )-methyl-dihydropyrazinoindolone scaffold our group has previously disclosed. The macrocyclic inhibitors bind Mcl-1 with subnanomolar affinity and offer improved potency in cell culture growth inhibition assays. Inhibitor 13 achieved tumor regression in a lung cancer-derived tumor xenograft model in mice as a monotherapy. The improved potency of the macrocyclic series allowed replacement of heretofore conserved indole carboxylic acid moiety, resulting in neutral inhibitors. Amide inhibitor 25 displayed a >10-fold increase in oral bioavailability as compared to acid-containing macrocyclic or acyclic inhibitors.


  • Organizational Affiliation
    • Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Avenue, 607 Light Hall, Nashville, Tennessee 37232-0146, United States.

Macromolecules
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
152Homo 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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CL3 (Subject of Investigation/LOI)
Query on A1CL3

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
7-[(4R,5S,6P)-7-chloro-10-[3-(4-chloro-3,5-dimethylphenoxy)propyl]-4-methyl-1-oxo-6-(1,3,5-trimethyl-1H-pyrazol-4-yl)-3,4-dihydropyrazino[1,2-a]indol-2(1H)-yl]-1-(2-methoxyethyl)-5-methyl-1H-indole-2-carboxylic acid
C42 H45 Cl2 N5 O5
ULTJCNHXGCJYCH-RUZDIDTESA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free:  0.258 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.613α = 90
b = 87.678β = 102.422
c = 50.348γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Boehringer Ingelheim Fonds (BIF)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release