Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 30.22 kDa 
• Atom Count: 2177 
• Modelled Residue Count: 246 
• Deposited Residue Count: 266 
• Unique protein chains: 2

6RJQ

Fragment AZ-006 binding at the TAZpS89/14-3-3 sigma interface

• DOI: 10.2210/pdb6RJQ/pdb

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


• Deposited: 2019-04-29 Released: 2020-06-17 
• Deposition Author(s): Genet, S., Wolter, M., Guillory, X., Somsen, B., Leysen, S., Castaldi, P., Ottmann, C., Patel, J.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.232 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 

Literature

Fragment-based Differential Targeting of PPI Stabilizer Interfaces.

Guillory, X., Wolter, M., Leysen, S., Neves, J.F., Kuusk, A., Genet, S., Somsen, B., Morrow, J.K., Rivers, E., van Beek, L., Patel, J., Goodnow, R., Schoenherr, H., Fuller, N., Cao, Q., Doveston, R.G., Brunsveld, L., Arkin, M.R., Castaldi, P., Boyd, H., Landrieu, I., Chen, H., Ottmann, C.

(2020) J Med Chem 63: 6694-6707

• PubMed: 32501690 
• DOI: 10.1021/acs.jmedchem.9b01942
• Primary Citation of Related Structures:  
  6RWS, 6RWU, 6RX2, 6RWH, 6RWI, 6S9Q, 6SIO, 6SIN, 6SIQ, 6SIP


• PubMed Abstract: 
  

Stabilization of protein-protein interactions (PPIs) holds great potential for therapeutic agents, as illustrated by the successful drugs rapamycin and lenalidomide. However, how such interface-binding molecules can be created in a rational, bottom-up manner is a largely unanswered question. We report here how a fragment-based approach can be used to identify chemical starting points for the development of small-molecule stabilizers that differentiate between two different PPI interfaces of the adapter protein 14-3-3. The fragments discriminately bind to the interface of 14-3-3 with the recognition motif of either the tumor suppressor protein p53 or the oncogenic transcription factor TAZ. This X-ray crystallography driven study shows that the rim of the interface of individual 14-3-3 complexes can be targeted in a differential manner with fragments that represent promising starting points for the development of specific 14-3-3 PPI stabilizers.

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Organizational Affiliation: 

Department of Organic Chemistry, University of Duisburg-Essen, 47057 Duisburg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein sigma	A	253	Homo sapiens	Mutation(s): 0  Gene Names: SFN, HME1
UniProt & NIH Common Fund Data Resources
Find proteins for P31947 (Homo sapiens) Explore P31947  Go to UniProtKB:  P31947
PHAROS:  P31947 GTEx:  ENSG00000175793

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TAZpS89	B [auth P]	13	Homo sapiens	Mutation(s): 0  Gene Names: WWTR1, TAZ
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZV5 (Homo sapiens) Explore Q9GZV5  Go to UniProtKB:  Q9GZV5
PHAROS:  Q9GZV5 GTEx:  ENSG00000018408

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JT2	C [auth A], D [auth A]	4-[[(2~{S})-1-azanylpropan-2-yl]amino]-6-(sulfanylmethyl)-1-benzothiophene-2-carboximidamide C13 H18 N4 S2 QYPDCDACLUDSPR-ZETCQYMHSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	B [auth P]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.232 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.05	α = 90
b = 112.09	β = 90
c = 62.65	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-04-29 
• Released Date: 2020-06-17 
Deposition Author(s): Genet, S., Wolter, M., Guillory, X., Somsen, B., Leysen, S., Castaldi, P., Ottmann, C., Patel, J.

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Funding Organization	Location	Grant Number
European Commission	Netherlands	--

Revision History  

• Version 1.0: 2020-06-17
  Type: Initial release
  
• Version 1.1: 2020-06-24
  Changes: Derived calculations
• Version 1.2: 2020-07-22
  Changes: Database references