3HCM

Crystal structure of human S100B in complex with S45

• PDB DOI: https://doi.org/10.2210/pdb3HCM/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-06 Released: 2010-02-02 
• Deposition Author(s): Mangani, S., Cesari, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.311 
• R-Value Work: 0.227 
• R-Value Observed: 0.231 

Starting Model: experimental

Literature

Fragmenting the S100B-p53 Interaction: Combined Virtual/Biophysical Screening Approaches to Identify Ligands

Agamennone, M., Cesari, L., Lalli, D., Turlizzi, E., Del Conte, R., Turano, P., Mangani, S., Padova, A.

(2010) ChemMedChem 5: 428-435

• PubMed: 20077460 
• DOI: https://doi.org/10.1002/cmdc.200900393
• Primary Citation of Related Structures:  
  3HCM


• PubMed Abstract: 
  

  S100B contributes to cell proliferation by binding the C terminus of p53 and inhibiting its tumor suppressor function. The use of multiple computational approaches to screen fragment libraries targeting the human S100B-p53 interaction site is reported. This in silico screening led to the identification of 280 novel prospective ligands. NMR spectroscopic experiments revealed specific binding at the p53 interaction site for a set of these compounds and confirmed their potential for further rational optimization. The X-ray crystal structure determined for one of the binders revealed key intermolecular interactions, thus paving the way for structure-based ligand optimization.

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Organizational Affiliation: 

Dipartimento di Scienze del Farmaco, Università "G. d'Annunzio", Via dei Vestini, 66013 Chieti, Italy.

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: 22.2 kDa 
• Atom Count: 1,611 
• Modelled Residue Count: 181 
• Deposited Residue Count: 184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein S100-B	A, B	92	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P04271 (Homo sapiens) Explore P04271  Go to UniProtKB:  P04271
PHAROS:  P04271 GTEx:  ENSG00000160307

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S45	E [auth A], I [auth B]	(3R)-3-[3-(4-chlorophenyl)-1,2,4-oxadiazol-5-yl]piperidine C13 H14 Cl N3 O ROGHUOMPUVCGAA-SNVBAGLBSA-N
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	C [auth A], D [auth A], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
S45	PDBBind:  3HCM	Kd: 5.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.311 
• R-Value Work: 0.227 
• R-Value Observed: 0.231 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.257	α = 90
b = 57.797	β = 111.41
c = 47.745	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-02 
Deposition Author(s): Mangani, S., Cesari, L.

Revision History  

• Version 1.0: 2010-02-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-04
  Changes: Data collection
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description