Selective targeting of disease-relevant protein binding domains by O-phosphorylated natural product derivatives

Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

Starting Model: experimental
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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Selective targeting of disease-relevant protein binding domains by o-phosphorylated natural product derivatives.

Graber, M.Janczyk, W.Sperl, B.Elumalai, N.Kozany, C.Hausch, F.Holak, T.A.Berg, T.

(2011) ACS Chem Biol 6: 1008-1014

  • DOI: https://doi.org/10.1021/cb2001796
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Phosphorylation-dependent protein binding domains are crucially important for intracellular signaling pathways and thus highly relevant targets in chemical biology. By screening of chemical libraries against 12 structurally diverse phosphorylation-dependent protein binding domains, we have identified fosfosal and dexamethasone-21-phosphate as selective inhibitors of two antitumor targets: the SH2 domain of the transcription factor STAT5b and the substrate-binding domain of the peptidyl-prolyl isomerase Pin1, respectively. Both compounds are phosphate prodrugs with documented clinical use as anti-inflammatory agents in humans and were discovered with a high hit rate from a small subgroup within the screening library. Our study indicates O-phosphorylation of appropriately preselected natural products or natural product derivatives as a generally applicable strategy for the identification of non-reactive and non-peptidic ligands of phosphorylation-dependent protein binding domains. Moreover, our data indicate that it would be advisable to monitor the bioactivities of clinically used prodrugs in their uncleaved state against phosphorylation-dependent protein binding domains.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1166Homo sapiensMutation(s): 1 
Gene Names: PIN1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13526 (Homo sapiens)
Explore Q13526 
Go to UniProtKB:  Q13526
GTEx:  ENSG00000127445 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13526
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 3T5

Download Ideal Coordinates CCD File 
B [auth A](11alpha,16alpha)-9-fluoro-11,17-dihydroxy-16-methyl-3,20-dioxopregna-1,4-dien-21-yl dihydrogen phosphate
C22 H30 F O8 P
Query on P6G

Download Ideal Coordinates CCD File 
C12 H26 O7
Binding Affinity Annotations 
IDSourceBinding Affinity
3T5 PDBBind:  3TC5 Kd: 6800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.40 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.36α = 90
b = 68.36β = 90
c = 79.37γ = 120
Software Package:
Software NamePurpose
MAR345data collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2011-11-02
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description