4DHS

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

PDB DOI: https://doi.org/10.2210/pdb4DHS/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.193
R-Value Work: 0.151
R-Value Observed: 0.153

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 27.11 kDa
Atom Count: 2,417
Modelled Residue Count: 228
Deposited Residue Count: 235
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31947
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y03 Query on Y03 Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	(2-{2-[(3,5-dichlorophenyl)amino]-2-oxoethoxy}phenyl)phosphonic acid C₁₄ H₁₂ Cl₂ N O₅ P CPVQZZLNMCVTEO-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

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

Binding Affinity Annotations
ID	Source	Binding Affinity
Y03	PDBBind: 4DHS	IC50: 1.60e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.193
R-Value Work: 0.151
R-Value Observed: 0.153
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.96	α = 90
b = 111.95	β = 90
c = 62.31	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-07-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-07-31
Type: Initial release
Version 1.1: 2013-09-04
Changes: Database references
Version 1.2: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary