4UE1

Structure of the stapled peptide YS-01 bound to MDM2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design.

Tan, Y.S., Reeks, J., Brown, C.J., Thean, D., Ferrer Gago, F.J., Yuen, T.Y., Goh, E.T., Lee, X.E., Jennings, C.E., Joseph, T.L., Lakshminarayanan, R., Lane, D.P., Noble, M.E., Verma, C.S.

(2016) J Phys Chem Lett 7: 3452-3457

  • DOI: 10.1021/acs.jpclett.6b01525
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Protein flexibility poses a major challenge in binding site identification. Several computational pocket detection methods that utilize small-molecule probes in molecular dynamics (MD) simulations have been developed to address this issue. Although t ...

    Protein flexibility poses a major challenge in binding site identification. Several computational pocket detection methods that utilize small-molecule probes in molecular dynamics (MD) simulations have been developed to address this issue. Although they have proven hugely successful at reproducing experimental structural data, their ability to predict new binding sites that are yet to be identified and characterized has not been demonstrated. Here, we report the use of benzenes as probe molecules in ligand-mapping MD (LMMD) simulations to predict the existence of two novel binding sites on the surface of the oncoprotein MDM2. One of them was serendipitously confirmed by biophysical assays and X-ray crystallography to be important for the binding of a new family of hydrocarbon stapled peptides that were specifically designed to target the other putative site. These results highlight the predictive power of LMMD and suggest that predictions derived from LMMD simulations can serve as a reliable basis for the identification of novel ligand binding sites in structure-based drug design.

    Organizational Affiliation: 

    Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR) , 30 Biopolis Street, #07-01 Matrix, Singapore 138671.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 UBIQUITIN-PROTEIN LIGASE MDM2
A, B, C, D
114Homo sapiensMutation(s): 2 
Gene Names: MDM2
EC: 2.3.2.27
Find proteins for Q00987 (Homo sapiens)
Go to Gene View: MDM2
Go to UniProtKB:  Q00987
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
YS-01
F, G, H, I
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
F, G, H, I
NON-POLYMERH2 N

--

2JN
Query on 2JN
F, G, H, I
D-PEPTIDE LINKINGC7 H15 N O2

--

ACE
Query on ACE
F, G, H, I
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.140 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.104α = 90.00
b = 69.462β = 101.96
c = 78.562γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2017-01-18
    Type: Database references