5C3F

Crystal structure of Mcl-1 bound to BID-MM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Hydrocarbon constrained peptides - understanding preorganisation and binding affinity.

Miles, J.A.Yeo, D.J.Rowell, P.Rodriguez-Marin, S.Pask, C.M.Warriner, S.L.Edwards, T.A.Wilson, A.J.

(2016) Chem Sci 7: 3694-3702

  • DOI: 10.1039/c5sc04048e
  • Primary Citation of Related Structures:  
    5C3F, 5C3G

  • PubMed Abstract: 
  • The development of constrained peptides represents an emerging strategy to generate peptide based probes and hits for drug-discovery that address challenging protein-protein interactions (PPIs). In this manuscript we report on the use of a novel α-al ...

    The development of constrained peptides represents an emerging strategy to generate peptide based probes and hits for drug-discovery that address challenging protein-protein interactions (PPIs). In this manuscript we report on the use of a novel α-alkenylglycine derived amino acid to synthesise hydrocarbon constrained BH3-family sequences (BIM and BID). Our biophysical and structural analyses illustrate that whilst the introduction of the constraint increases the population of the bioactive α-helical conformation of the peptide in solution, it does not enhance the inhibitory potency against pro-apoptotic Bcl-x L and Mcl-1 PPIs. SPR analyses indicate binding occurs via an induced fit mechanism whilst X-ray analyses illustrate none of the key interactions between the helix and protein are disturbed. The behaviour derives from enthalpy-entropy compensation which may be considered in terms of the ground state energies of the unbound constrained and unconstrained peptides; this has implications for the design of preorganised peptides to target protein-protein interactions.


    Organizational Affiliation

    Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . Email: T.A.Edwards@leeds.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Induced myeloid leukemia cell differentiation protein Mcl-1A156Homo sapiensMutation(s): 0 
Gene Names: MCL1BCL2L3
Find proteins for Q07820 (Homo sapiens)
Explore Q07820 
Go to UniProtKB:  Q07820
NIH Common Fund Data Resources
PHAROS  Q07820
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BID-MMB24Homo sapiensMutation(s): 0 
Gene Names: BID
Find proteins for P55957 (Homo sapiens)
Explore P55957 
Go to UniProtKB:  P55957
NIH Common Fund Data Resources
PHAROS  P55957
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NLE
Query on NLE
BL-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.83α = 90
b = 37.02β = 90
c = 56.92γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
REFMACphasing
XDSdata reduction
xia2data scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited KingdomERC-StG-240324

Revision History 

  • Version 1.0: 2016-04-20
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Database references