X-ray structure of bovine SBi279,Ca(2+)-S100B

Experimental Data Snapshot

  • Resolution: 1.98 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

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This is version 1.3 of the entry. See complete history


Small molecules bound to unique sites in the target protein binding cleft of calcium-bound S100B as characterized by nuclear magnetic resonance and X-ray crystallography.

Charpentier, T.H.Wilder, P.T.Liriano, M.A.Varney, K.M.Zhong, S.Coop, A.Pozharski, E.MacKerell, A.D.Toth, E.A.Weber, D.J.

(2009) Biochemistry 48: 6202-6212

  • DOI: https://doi.org/10.1021/bi9005754
  • Primary Citation of Related Structures:  
    3GK1, 3GK2, 3GK4

  • PubMed Abstract: 

    Structural studies are part of a rational drug design program aimed at inhibiting the S100B-p53 interaction and restoring wild-type p53 function in malignant melanoma. To this end, structures of three compounds (SBi132, SBi1279, and SBi523) bound to Ca(2+)-S100B were determined by X-ray crystallography at 2.10 A (R(free) = 0.257), 1.98 A (R(free) = 0.281), and 1.90 A (R(free) = 0.228) resolution, respectively. Upon comparison, SBi132, SBi279, and SBi523 were found to bind in distinct locations and orientations within the hydrophobic target binding pocket of Ca(2+)-S100B with minimal structural changes observed for the protein upon complex formation with each compound. Specifically, SBi132 binds nearby residues in loop 2 (His-42, Phe-43, and Leu-44) and helix 4 (Phe-76, Met-79, Ile-80, Ala-83, Cys-84, Phe-87, and Phe-88), whereas SBi523 interacts with a separate site defined by residues within loop 2 (Ser-41, His-42, Phe-43, Leu-44, Glu-45, and Glu-46) and one residue on helix 4 (Phe-87). The SBi279 binding site on Ca(2+)-S100B overlaps the SBi132 and SBi523 sites and contacts residues in both loop 2 (Ser-41, His-42, Phe-43, Leu-44, and Glu-45) and helix 4 (Ile-80, Ala-83, Cys-84, Phe-87, and Phe-88). NMR data, including saturation transfer difference (STD) and (15)N backbone and (13)C side chain chemical shift perturbations, were consistent with the X-ray crystal structures and demonstrated the relevance of all three small molecule-S100B complexes in solution. The discovery that SBi132, SBi279, and SBi523 bind to proximal sites on Ca(2+)-S100B could be useful for the development of a new class of molecule(s) that interacts with one or more of these binding sites simultaneously, thereby yielding novel tight binding inhibitors specific for blocking protein-protein interactions involving S100B.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Maryland School of Medicine, 108 North Greene Street, Baltimore, Maryland 21201, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein S100-B92Bos 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
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
27A PDBBind:  3GK2 Kd: 2.00e+6 (nM) from 1 assay(s)
Binding MOAD:  3GK2 Kd: 2.00e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.98 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.224α = 90
b = 91.158β = 90
c = 58.649γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description