4DHO | pdb_00004dho

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

PDB DOI: https://doi.org/10.2210/pdb4DHO/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: 1.70 Å
R-Value Free:
0.203 (Depositor), 0.201 (DCC)
R-Value Work:
0.160 (Depositor), 0.158 (DCC)
R-Value Observed:
0.162 (Depositor)

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

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: 27.08 kDa
Atom Count: 2,403
Modeled Residue Count: 228
Deposited Residue Count: 235
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31947
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y09 Query on Y09 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	(2-{2-[(3-methoxyphenyl)amino]-2-oxoethoxy}phenyl)phosphonic acid C₁₅ H₁₆ N O₆ P RAGQGGPMVFHHRB-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [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] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.203 (Depositor), 0.201 (DCC)
R-Value Work: 0.160 (Depositor), 0.158 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.94	α = 90
b = 111.69	β = 90
c = 62.29	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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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: 2024-02-28
Changes: Data collection, Database references, Derived calculations