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 

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:  

  • 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-xL 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

    School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . Email: A.J.Wilson@leeds.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Induced myeloid leukemia cell differentiation protein Mcl-1
A
156Homo sapiensMutation(s): 0 
Gene Names: MCL1 (BCL2L3)
Find proteins for Q07820 (Homo sapiens)
Go to Gene View: MCL1
Go to UniProtKB:  Q07820
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BID-MM
B
24Homo sapiensMutation(s): 0 
Gene Names: BID
Find proteins for P55957 (Homo sapiens)
Go to Gene View: BID
Go to UniProtKB:  P55957
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NLE
Query on NLE
B
L-PEPTIDE LINKINGC6 H13 N O2LEU
ACE
Query on ACE
B
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.162 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 80.830α = 90.00
b = 37.020β = 90.00
c = 56.920γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
xia2data scaling
REFMACphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references