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

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