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 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    5VKC, 6B4U, 6B4L

  • 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Induced myeloid leukemia cell differentiation protein Mcl-1A, B157Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9EA (Subject of Investigation/LOI)
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
VKKQBUSCPZGZBT-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
BUSTERrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
MOLREPphasing

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