4G35 | pdb_00004g35

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

• PDB DOI: https://doi.org/10.2210/pdb4G35/pdb

• Classification: Apoptosis/Inhibitor
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-07-13 Released: 2012-12-05 
• Deposition Author(s): Drake, E., Edwardraja, S., Lin, Q., Gulick, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.239 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.192 (Depositor) 
• R-Value Observed: 
  0.194 (Depositor) 

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

• PubMed: 22920569 
• DOI: https://doi.org/10.1021/ja306864v
• Primary Citation Related Structures: 
  4G35


• 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-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.

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Organizational Affiliation: 
• Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.16 kDa 
• Atom Count: 1,255 
• Modeled Residue Count: 150 
• Deposited Residue Count: 186 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Induced myeloid leukemia cell differentiation protein Mcl-1 homolog	A	165	Mus musculus	Mutation(s): 0  Gene Names: Mcl1
UniProt & NIH Common Fund Data Resources
Find proteins for P97287 (Mus musculus) Explore P97287  Go to UniProtKB:  P97287
IMPC:  MGI:101769

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Noxa BH3 peptide (cysteine-mediated cross-linked)	B	21	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4BP	C [auth B]	4,4'-bis(bromomethyl)biphenyl C14 H12 Br2 HMUGRILXVBKBID-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000921	B	Noxa BH3 peptide (cysteine-mediated cross-linked)	Polypeptide / Anticancer

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.239 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.192 (Depositor) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.04	α = 90
b = 47.97	β = 90
c = 68.6	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-05 
Deposition Author(s): Drake, E., Edwardraja, S., Lin, Q., Gulick, A.M.

Revision History  

• Version 1.0: 2012-12-05
  Type: Initial release
  
• Version 1.1: 2013-06-26
  Changes: Derived calculations
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary