6RWH

Fragment AZ-007 binding at a primary and secondary binding site of the the p53pT387/14-3-3 sigma complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

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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:  
    6R5L, 6SIO, 6SIN, 6SIQ, 6SIP, 6SLX, 6SLW, 6SLV, 6RHC, 6RJL, 6RKI, 6RKK, 6RKM, 6RK8, 6RJZ, 6RJQ, 6RL3, 6RL4, 6RL6, 6RM5, 6RM7, 6RP6, 6S40, 6S3C, 6S39, 6RWS, 6RWU, 6RX2, 6RWH, 6RWI, 6S9Q

  • 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 sigmaA253Homo 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
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  • 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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KLB (Subject of Investigation/LOI)
Query on KLB

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]5-(1~{H}-imidazol-5-yl)-4-phenyl-thiophene-2-carboximidamide
C14 H12 N4 S
FXABOLLAJZFHEL-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A], G [auth P]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 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: 1.68 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.642α = 90
b = 112.176β = 90
c = 63.089γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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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