4DHP

Small-molecule inhibitors of 14-3-3 protein-protein interactions from virtual screening

• PDB DOI: https://doi.org/10.2210/pdb4DHP/pdb

• Classification: PROTEIN BINDING/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-01-30 Released: 2013-07-31 
• Deposition Author(s): Thiel, P., Roeglin, L., Kohlbacher, O., Ottmann, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.196 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 

Literature

Virtual screening and experimental validation reveal novel small-molecule inhibitors of 14-3-3 protein-protein interactions.

Thiel, P., Roglin, L., Meissner, N., Hennig, S., Kohlbacher, O., Ottmann, C.

(2013) Chem Commun (Camb) 49: 8468-8470

• PubMed: 23939230 
• DOI: https://doi.org/10.1039/c3cc44612c
• Primary Citation of Related Structures:  
  3T0L, 3T0M, 4DHM, 4DHN, 4DHO, 4DHP, 4DHQ, 4DHR, 4DHS, 4DHT, 4DHU


• PubMed Abstract: 
  

  We report first non-covalent and exclusively extracellular inhibitors of 14-3-3 protein-protein interactions identified by virtual screening. Optimization by crystal structure analysis and in vitro binding assays yielded compounds capable of disrupting the interaction of 14-3-3σ with aminopeptidase N in a cellular assay.

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Organizational Affiliation: 

Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Straße 15, D-44227 Dortmund, Germany.

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: 27.2 kDa 
• Atom Count: 2,475 
• Modelled Residue Count: 228 
• Deposited Residue Count: 235 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein sigma	A	235	Homo sapiens	Mutation(s): 0  Gene Names: HME1, SFN
UniProt & NIH Common Fund Data Resources
Find proteins for P31947 (Homo sapiens) Explore P31947  Go to UniProtKB:  P31947
PHAROS:  P31947 GTEx:  ENSG00000175793

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y07	J [auth A]	[2-(2-{[2-chloro-5-(trifluoromethyl)phenyl]amino}-2-oxoethoxy)phenyl]phosphonic acid C15 H12 Cl F3 N O5 P JQGAEOCOPMLHLZ-UHFFFAOYSA-N
GOL	I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
Y07	PDBBind:  4DHP	IC50: 3.60e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.196 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.25	α = 90
b = 112.23	β = 90
c = 62.42	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-31 
Deposition Author(s): Thiel, P., Roeglin, L., Kohlbacher, O., Ottmann, C.

Revision History  

• Version 1.0: 2013-07-31
  Type: Initial release
  
• Version 1.1: 2013-09-04
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary