Crystal Structure of Calcium-loaded S100B bound to SC124

Experimental Data Snapshot

  • Resolution: 1.58 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


Covalent Small Molecule Inhibitors of Ca(2+)-Bound S100B.

Cavalier, M.C.Pierce, A.D.Wilder, P.T.Alasady, M.J.Hartman, K.G.Neau, D.B.Foley, T.L.Jadhav, A.Maloney, D.J.Simeonov, A.Toth, E.A.Weber, D.J.

(2014) Biochemistry 53: 6628-6640

  • DOI: https://doi.org/10.1021/bi5005552
  • Primary Citation of Related Structures:  
    4PDZ, 4PE0, 4PE1, 4PE4, 4PE7

  • PubMed Abstract: 

    Elevated levels of the tumor marker S100B are observed in malignant melanoma, and this EF-hand-containing protein was shown to directly bind wild-type (wt) p53 in a Ca(2+)-dependent manner, dissociate the p53 tetramer, and inhibit its tumor suppression functions. Likewise, inhibiting S100B with small interfering RNA (siRNA(S100B)) is sufficient to restore wild-type p53 levels and its downstream gene products and induce the arrest of cell growth and UV-dependent apoptosis in malignant melanoma. Therefore, it is a goal to develop S100B inhibitors (SBiXs) that inhibit the S100B-p53 complex and restore active p53 in this deadly cancer. Using a structure-activity relationship by nuclear magnetic resonance approach (SAR by NMR), three persistent binding pockets are found on S100B, termed sites 1-3. While inhibitors that simultaneously bind sites 2 and 3 are in place, no molecules that simultaneously bind all three persistent sites are available. For this purpose, Cys84 was used in this study as a potential means to bridge sites 1 and 2 because it is located in a small crevice between these two deeper pockets on the protein. Using a fluorescence polarization competition assay, several Cys84-modified S100B complexes were identified and examined further. For five such SBiX-S100B complexes, crystallographic structures confirmed their covalent binding to Cys84 near site 2 and thus present straightforward chemical biology strategies for bridging sites 1 and 3. Importantly, one such compound, SC1982, showed an S100B-dependent death response in assays with WM115 malignant melanoma cells, so it will be particularly useful for the design of SBiX molecules with improved affinity and specificity.

  • Organizational Affiliation

    Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein S100-B
A, B
92Bos taurusMutation(s): 0 
Gene Names: S100B
Find proteins for P02638 (Bos taurus)
Explore P02638 
Go to UniProtKB:  P02638
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02638
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.58 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.649α = 90
b = 56.463β = 110.1
c = 48.269γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
Blu-Icedata collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM58888
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA107331
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA154274

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-11-05
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description