5DKR

Crystal Structure of Calcium-loaded S100B bound to SBi29


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.742 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Small Molecule Inhibitors of Ca(2+)-S100B Reveal Two Protein Conformations.

Cavalier, M.C.Ansari, M.I.Pierce, A.D.Wilder, P.T.McKnight, L.E.Raman, E.P.Neau, D.B.Bezawada, P.Alasady, M.J.Charpentier, T.H.Varney, K.M.Toth, E.A.MacKerell, A.D.Coop, A.Weber, D.J.

(2016) J.Med.Chem. 59: 592-608

  • DOI: 10.1021/acs.jmedchem.5b01369
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The drug pentamidine inhibits calcium-dependent complex formation with p53 ((Ca)S100B·p53) in malignant melanoma (MM) and restores p53 tumor suppressor activity in vivo. However, off-target effects associated with this drug were problematic in MM pat ...

    The drug pentamidine inhibits calcium-dependent complex formation with p53 ((Ca)S100B·p53) in malignant melanoma (MM) and restores p53 tumor suppressor activity in vivo. However, off-target effects associated with this drug were problematic in MM patients. Structure-activity relationship (SAR) studies were therefore completed here with 23 pentamidine analogues, and X-ray structures of (Ca)S100B·inhibitor complexes revealed that the C-terminus of S100B adopts two different conformations, with location of Phe87 and Phe88 being the distinguishing feature and termed the "FF-gate". For symmetric pentamidine analogues ((Ca)S100B·5a, (Ca)S100B·6b) a channel between sites 1 and 2 on S100B was occluded by residue Phe88, but for an asymmetric pentamidine analogue ((Ca)S100B·17), this same channel was open. The (Ca)S100B·17 structure illustrates, for the first time, a pentamidine analog capable of binding the "open" form of the "FF-gate" and provides a means to block all three "hot spots" on (Ca)S100B, which will impact next generation (Ca)S100B·p53 inhibitor design.


    Organizational Affiliation

    Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive, Rockville, Maryland 20850, United States.,Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine , Baltimore, Maryland 21201, United States.,Computer Aided Drug Design Center, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States.,Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States.,NE-CAT , Argonne Illinois 60439, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein S100-B
A, B
92Bos taurusMutation(s): 0 
Gene Names: S100B
Find proteins for P02638 (Bos taurus)
Go to Gene View: S100B
Go to UniProtKB:  P02638
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5CZ
Query on 5CZ

Download SDF File 
Download CCD File 
A
2-[4-(4-carbamimidoylphenoxy)phenyl]-1H-indole-6-carboximidamide
C22 H19 N5 O
OSSYTOVYXCAWPG-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5CZIC50: 66600 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.742 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.745α = 90.00
b = 47.443β = 90.00
c = 90.343γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesCA154274
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM58888
National Institutes of Health/National Cancer InstituteUnited StatesCA107331

Revision History 

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-02-10
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations, Refinement description