Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

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

Macromolecule Content

• Total Structure Weight: 20337.17 
• Atom Count: 1281 
• Residue Count: 179 
• Unique protein chains: 2

3MK8

The MCL-1 BH3 Helix is an Exclusive MCL-1 Inhibitor and Apoptosis Sensitizer

• DOI: 10.2210/pdb3MK8/pdb

• Classification: APOPTOSIS/APOPTOSIS REGULATOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 2 


• Deposited: 2010-04-14 Released: 2010-06-23 
• Deposition Author(s): Stewart, M., Fire, E., Keating, A.E., Walensky, L.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.321 Å
• R-Value Free: 0.275 
• R-Value Work: 0.231 

Literature

The MCL-1 BH3 helix is an exclusive MCL-1 inhibitor and apoptosis sensitizer.

Stewart, M.L., Fire, E., Keating, A.E., Walensky, L.D.

(2010) Nat.Chem.Biol. 6: 595-601

• PubMed: 20562877 
• DOI: 10.1038/nchembio.391


• PubMed Abstract: 
  

The development of selective inhibitors for discrete anti-apoptotic BCL-2 family proteins implicated in pathologic cell survival remains a formidable but pressing challenge. Such precisely tailored compounds would serve as molecular probes and targeted therapies to study and treat human diseases driven by specific anti-apoptotic blockades. In particular, MCL-1 has emerged as a major resistance factor in human cancer. By screening a library of stabilized alpha-helix of BCL-2 domains (SAHBs), we determined that the MCL-1 BH3 helix is itself a potent and exclusive MCL-1 inhibitor. X-ray crystallography and mutagenesis studies defined key binding and specificity determinants, including the capacity to harness the hydrocarbon staple to optimize affinity while preserving selectivity. MCL-1 SAHB directly targets MCL-1, neutralizes its inhibitory interaction with pro-apoptotic BAK and sensitizes cancer cells to caspase-dependent apoptosis. By leveraging nature's solution to ligand selectivity, we generated an MCL-1-specific agent that defines the structural and functional features of targeted MCL-1 inhibition.

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Organizational Affiliation: 

Department of Pediatric Oncology, Dana-Farber Cancer Institute and Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Induced myeloid leukemia cell differentiation protein Mcl-1	A	158	Homo sapiens	Mutation(s): 0  Gene Names: MCL1 (BCL2L3)
Find proteins for Q07820 (Homo sapiens) Go to Gene View: MCL1 Go to UniProtKB:  Q07820

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Induced myeloid leukemia cell differentiation protein Mcl-1	B	21	Homo sapiens	Mutation(s): 2  Gene Names: MCL1 (BCL2L3)
Find proteins for Q07820 (Homo sapiens) Go to Gene View: MCL1 Go to UniProtKB:  Q07820

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MK8	B	L-peptide linking	C7 H15 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.321 Å
• R-Value Free: 0.275 
• R-Value Work: 0.231 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 44.505	α = 90.00
b = 56.866	β = 90.00
c = 63.984	γ = 90.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
HKL-2000	data scaling
HKL-2000	data reduction
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
HKL-2000	data collection
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-04-14 
• Released Date: 2010-06-23 
• Deposition Author(s): Stewart, M., Fire, E., Keating, A.E., Walensky, L.D.

Revision History 

• Version 1.0: 2010-06-23
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2017-11-08
  Type: Refinement description