4G35

Mcl-1 in complex with a biphenyl cross-linked Noxa peptide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Rational design of proteolytically stable, cell-permeable peptide-based selective Mcl-1 inhibitors.

Muppidi, A.Doi, K.Edwardraja, S.Drake, E.J.Gulick, A.M.Wang, H.G.Lin, Q.

(2012) J.Am.Chem.Soc. 134: 14734-14737

  • DOI: 10.1021/ja306864v

  • PubMed Abstract: 
  • Direct chemical modifications provide a simple and effective means to "translate" bioactive helical peptides into potential therapeutics targeting intracellular protein-protein interactions. We previously showed that distance-matching bisaryl cross-l ...

    Direct chemical modifications provide a simple and effective means to "translate" bioactive helical peptides into potential therapeutics targeting intracellular protein-protein interactions. We previously showed that distance-matching bisaryl cross-linkers can reinforce peptide helices containing two cysteines at the i and i+7 positions and confer cell permeability to the cross-linked peptides. Here we report the first crystal structure of a biphenyl-cross-linked Noxa peptide in complex with its target Mcl-1 at 2.0 Å resolution. Guided by this structure, we remodeled the surface of this cross-linked peptide through side-chain substitution and N-methylation and obtained a pair of cross-linked peptides with substantially increased helicity, cell permeability, proteolytic stability, and cell-killing activity in Mcl-1-overexpressing U937 cells.


    Organizational Affiliation

    Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Induced myeloid leukemia cell differentiation protein Mcl-1 homolog
A
165Mus musculusGene Names: Mcl1
Find proteins for P97287 (Mus musculus)
Go to UniProtKB:  P97287
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Noxa BH3 peptide (cysteine-mediated cross-linked)
B
21N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4BP
Query on 4BP

Download SDF File 
Download CCD File 
B
4,4'-bis(bromomethyl)biphenyl
C14 H12 Br2
HMUGRILXVBKBID-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000921
Query on PRD_000921
BNoxa BH3 peptide (cysteine-mediated cross-linked)Polypeptide / Anticancer

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.040α = 90.00
b = 47.970β = 90.00
c = 68.600γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-05
    Type: Initial release
  • Version 1.1: 2013-06-26
    Type: Derived calculations