6VBX

Crystal structure of Mcl-1 in complex with 138E12 peptide, Lys-covalent antagonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Design, Synthesis, and Structural Characterization of Lysine Covalent BH3 Peptides Targeting Mcl-1.

Gambini, L.Udompholkul, P.Baggio, C.Muralidharan, A.Kenjic, N.Assar, Z.Perry, J.J.P.Pellecchia, M.

(2021) J Med Chem 64: 4903-4912

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00005
  • Primary Citation of Related Structures:  
    6VBX

  • PubMed Abstract: 

    Modulating disease-relevant protein-protein interactions (PPIs) using pharmacological tools is a critical step toward the design of novel therapeutic strategies. Over the years, however, targeting PPIs has proven a very challenging task owing to the large interfacial areas. Our recent efforts identified possible novel routes for the design of potent and selective inhibitors of PPIs using a structure-based design of covalent inhibitors targeting Lys residues. In this present study, we report on the design, synthesis, and characterizations of the first Lys-covalent BH3 peptide that has a remarkable affinity and selectivity for hMcl-1 over the closely related hBfl-1 protein. Our structural studies, aided by X-ray crystallography, provide atomic-level details of the inhibitor interactions that can be used to further translate these discoveries into novel generation, Lys-covalent pro-apoptotic agents.


  • Organizational Affiliation

    Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, 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-1156Homo 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

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Synthetic peptide13synthetic constructMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O43521 (Homo sapiens)
Explore O43521 
Go to UniProtKB:  O43521
PHAROS:  O43521
GTEx:  ENSG00000153094 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43521
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
QX7
Query on QX7
B
L-PEPTIDE LINKINGC13 H15 F N2 O6 SALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.607α = 90
b = 54.607β = 90
c = 97.838γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA168517

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release
  • Version 1.1: 2021-06-09
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description