5VKC

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

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: 10.1021/jm501258m
  • Primary Citation of Related Structures:  

  • 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 pro ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Induced myeloid leukemia cell differentiation protein Mcl-1
A, B
157Homo sapiensMutation(s): 0 
Gene Names: MCL1 (BCL2L3)
Find proteins for Q07820 (Homo sapiens)
Go to Gene View: MCL1
Go to UniProtKB:  Q07820
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
9EA
Query on 9EA
Download SDF File 
Download CCD File 
A, 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
VKKQBUSCPZGZBT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.201 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 63.920α = 90.00
b = 63.920β = 90.00
c = 91.400γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTERrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-08-23
    Type: Data collection