6SIQ

Fragment AZ-012 binding at the p53pT387/14-3-3 sigma interface


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.182 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: 10.1021/acs.jmedchem.9b01942
  • Primary Citation of Related Structures:  
    6RWS, 6RWU, 6RX2, 6RWH, 6RWI, 6S9Q, 6SIO, 6SIN, 6SIQ, 6SIP, 6SLX, 6SLW, 6SLV, 6RHC, 6RJL, 6RKI, 6RKK, 6RKM, 6RK8, 6RJZ, 6RJQ, 6RL3, 6RL4, 6RL6, 6RM5, 6RM7, 6RP6, 6S40, 6S3C, 6S39, 6R5L

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
14-3-3 protein sigmaA236Homo sapiensMutation(s): 0 
Gene Names: SFNHME1
UniProt & NIH Common Fund Data Resources
Find proteins for P31947 (Homo sapiens)
Explore P31947 
Go to UniProtKB:  P31947
PHAROS:  P31947
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cellular tumor antigen p53B [auth P]12Homo sapiensMutation(s): 0 
Gene Names: TP53P53
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens)
Explore P04637 
Go to UniProtKB:  P04637
PHAROS:  P04637
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LF5 (Subject of Investigation/LOI)
Query on LF5

Download Ideal Coordinates CCD File 
D [auth A], E [auth A]4-chloranyl-7-propan-2-yloxy-1-benzothiophene-2-carboximidamide
C12 H13 Cl N2 O S
RFZOPKHHJPMIJW-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
B [auth P]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.182 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.34α = 90
b = 112.004β = 90
c = 62.572γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionNetherlands--

Revision History  (Full details and data files)

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