4DRI

Co-crystal structure of the PPIase domain of FKBP51, Rapamycin and the FRB fragment of mTOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Large FK506-Binding Proteins Shape the Pharmacology of Rapamycin.

Marz, A.M.Fabian, A.K.Kozany, C.Bracher, A.Hausch, F.

(2013) Mol Cell Biol 33: 1357-1367

  • DOI: 10.1128/MCB.00678-12
  • Primary Citation of Related Structures:  
    4DRH, 4DRI, 4DRJ

  • PubMed Abstract: 
  • The immunosuppressant and anticancer drug rapamycin works by inducing inhibitory protein complexes with the kinase mTOR, an important regulator of growth and proliferation. The obligatory accessory partner of rapamycin is believed to be FK506-binding protein 12 (FKBP12) ...

    The immunosuppressant and anticancer drug rapamycin works by inducing inhibitory protein complexes with the kinase mTOR, an important regulator of growth and proliferation. The obligatory accessory partner of rapamycin is believed to be FK506-binding protein 12 (FKBP12). Here we show that rapamycin complexes of larger FKBP family members can tightly bind to mTOR and potently inhibit its kinase activity. Cocrystal structures with FKBP51 and FKBP52 reveal the modified molecular binding mode of these alternative ternary complexes in detail. In cellular model systems, FKBP12 can be functionally replaced by larger FKBPs. When the rapamycin dosage is limiting, mTOR inhibition of S6K phosphorylation can be enhanced by FKBP51 overexpression in mammalian cells, whereas FKBP12 is dispensable. FKBP51 could also enable the rapamycin-induced hyperphosphorylation of Akt, which depended on higher FKBP levels than rapamycin-induced inhibition of S6K phosphorylation. These insights provide a mechanistic rationale for preferential mTOR inhibition in specific cell or tissue types by engaging specific FKBP homologs.


    Organizational Affiliation

    Max Planck Institute of Psychiatry, Department of Chemical Genomics, Munich, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP5A144Homo sapiensMutation(s): 0 
Gene Names: AIG6FKBP5FKBP51
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q13451 (Homo sapiens)
Explore Q13451 
Go to UniProtKB:  Q13451
PHAROS:  Q13451
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13451
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase mTORB98Homo sapiensMutation(s): 0 
Gene Names: FRAPFRAP1FRAP2MTORRAFT1RAPT1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P42345 (Homo sapiens)
Explore P42345 
Go to UniProtKB:  P42345
PHAROS:  P42345
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42345
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RAP
Query on RAP

Download Ideal Coordinates CCD File 
C [auth A]RAPAMYCIN IMMUNOSUPPRESSANT DRUG
C51 H79 N O13
QFJCIRLUMZQUOT-HPLJOQBZSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
RAP BindingDB:  4DRI Ki: 3 (nM) from 1 assay(s)
Kd: 0.6 (nM) from 1 assay(s)
IC50: min: 0.05, max: 430 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.503α = 90
b = 59.554β = 90
c = 67.787γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-06
    Type: Initial release
  • Version 1.1: 2013-03-27
    Changes: Database references