Mcl-1 complexed with small molecules

  • Classification: APOPTOSIS
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2017-12-14 Released: 2018-01-31 
  • Deposition Author(s): Zhao, B.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Resolution: 2.75 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Optimization of Potent and Selective Tricyclic Indole Diazepinone Myeloid Cell Leukemia-1 Inhibitors Using Structure-Based Design.

Shaw, S.Bian, Z.Zhao, B.Tarr, J.C.Veerasamy, N.Jeon, K.O.Belmar, J.Arnold, A.L.Fogarty, S.A.Perry, E.Sensintaffar, J.L.Camper, D.V.Rossanese, O.W.Lee, T.Olejniczak, E.T.Fesik, S.W.

(2018) J Med Chem 61: 2410-2421

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b01155
  • Primary Citation of Related Structures:  
    6BW2, 6BW8

  • PubMed Abstract: 

    Myeloid cell leukemia 1 (Mcl-1), an antiapoptotic member of the Bcl-2 family of proteins, has emerged as an attractive target for cancer therapy. Mcl-1 upregulation is often found in many human cancers and is associated with high tumor grade, poor survival, and resistance to chemotherapy. Here, we describe a series of potent and selective tricyclic indole diazepinone Mcl-1 inhibitors that were discovered and further optimized using structure-based design. These compounds exhibit picomolar binding affinity and mechanism-based cellular efficacy, including growth inhibition and caspase induction in Mcl-1-sensitive cells. Thus, they represent useful compounds to study the implication of Mcl-1 inhibition in cancer and serve as potentially useful starting points toward the discovery of anti-Mcl-1 therapeutics.

  • Organizational Affiliation

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

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, C, D
158Homo 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
Query on ECY

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth D]
3-({11-[3-(4-chloro-3,5-dimethylphenoxy)propyl]-1-oxo-7-(1,3,5-trimethyl-1H-pyrazol-4-yl)-4,5-dihydro-1H-[1,4]diazepino[1,2-a]indol-2(3H)-yl}methyl)benzoic acid
C37 H39 Cl N4 O4
Binding Affinity Annotations 
IDSourceBinding Affinity
ECY BindingDB:  6BW2 Ki: min: 7, max: 50 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.75 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.284α = 90
b = 134.369β = 90.04
c = 96.561γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2018-01-31 
  • Deposition Author(s): Zhao, B.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesBOA29XS129TO22

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-03-21
    Changes: Database references
  • Version 1.2: 2018-04-04
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description