5DKQ | pdb_00005dkq

Crystal Structure of Calcium-loaded S100B bound to SBi4214

• PDB DOI: https://doi.org/10.2210/pdb5DKQ/pdb

• Classification: METAL BINDING PROTEIN/INHIBITOR
• Organism(s): Bos taurus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-09-03 Released: 2016-01-20 
• Deposition Author(s): 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., Varney, K.M., Toth, E.A., MacKerell Jr., A.D., Coop, A., Weber, D.J.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.230 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

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

• PubMed: 26727270 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b01369
• Primary Citation Related Structures: 
  5DKN, 5DKQ, 5DKR


• 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 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.

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Organizational Affiliation: 
• 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.
Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive, Rockville, Maryland 20850, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 11.18 kDa 
• Atom Count: 884 
• Modeled Residue Count: 91 
• Deposited Residue Count: 92 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein S100-B	A	92	Bos taurus	Mutation(s): 0  Gene Names: S100B
UniProt
Find proteins for P02638 (Bos taurus) Explore P02638  Go to UniProtKB:  P02638

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5D0	D [auth A]	2,2'-[pentane-1,5-diylbis(oxybenzene-4,1-diyl)]di-1,4,5,6-tetrahydropyrimidine C25 H32 N4 O2 KPYLNHFSSDNDFO-UHFFFAOYSA-N
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.230 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.485	α = 90
b = 63.485	β = 90
c = 48.275	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): 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., Varney, K.M., Toth, E.A., MacKerell Jr., A.D., Coop, A., Weber, D.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA154274
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM58888
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA107331

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2016-02-10
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence, Database references, Derived calculations, Refinement description
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description