Crystal structure of MCL-1 in complex with a BIM competitive inhibitor

Experimental Data Snapshot

  • Resolution: 2.31 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

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Ligand Structure Quality Assessment 

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Structure-guided design of a series of MCL-1 inhibitors with high affinity and selectivity.

Bruncko, M.Wang, L.Sheppard, G.S.Phillips, D.C.Tahir, S.K.Xue, J.Erickson, S.Fidanze, S.Fry, E.Hasvold, L.Jenkins, G.J.Jin, S.Judge, R.A.Kovar, P.J.Madar, D.Nimmer, P.Park, C.Petros, A.M.Rosenberg, S.H.Smith, M.L.Song, X.Sun, C.Tao, Z.F.Wang, X.Xiao, Y.Zhang, H.Tse, C.Leverson, J.D.Elmore, S.W.Souers, A.J.

(2015) J Med Chem 58: 2180-2194

  • DOI: https://doi.org/10.1021/jm501258m
  • Primary Citation of Related Structures:  
    5VKC, 6B4L, 6B4U

  • PubMed Abstract: 

    Myeloid cell leukemia 1 (MCL-1) is a BCL-2 family protein that has been implicated in the progression and survival of multiple tumor types. Herein we report a series of MCL-1 inhibitors that emanated from a high throughput screening (HTS) hit and progressed via iterative cycles of structure-guided design. Advanced compounds from this series exhibited subnanomolar affinity for MCL-1 and excellent selectivity over other BCL-2 family proteins as well as multiple kinases and GPCRs. In a MCL-1 dependent human tumor cell line, administration of compound 30b rapidly induced caspase activation with associated loss in cell viability. The small molecules described herein thus comprise effective tools for studying MCL-1 biology.

  • Organizational Affiliation

    AbbVie Inc. , 1 North Waukegan Road, North Chicago, Illinois 60064, 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
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 9EA

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
7-(3-{[4-(4-acetylpiperazin-1-yl)phenoxy]methyl}-1,5-dimethyl-1H-pyrazol-4-yl)-3-{3-[(naphthalen-1-yl)oxy]propyl}-1-[(pyridin-3-yl)methyl]-1H-indole-2-carboxylic acid
C46 H46 N6 O5
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
N [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
9EA BindingDB:  5VKC Ki: min: 1.8, max: 98 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.31 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.92α = 90
b = 63.92β = 90
c = 91.4γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-08-23
    Changes: Data collection
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references, Derived calculations