4JT5

mTORdeltaN-mLST8-pp242 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

mTOR kinase structure, mechanism and regulation.

Yang, H.Rudge, D.G.Koos, J.D.Vaidialingam, B.Yang, H.J.Pavletich, N.P.

(2013) Nature 497: 217-223

  • DOI: 10.1038/nature12122
  • Primary Citation of Related Structures:  
    4JT6, 4JSV, 4JSX, 4JSN, 4JSP, 4JT5

  • PubMed Abstract: 
  • The mammalian target of rapamycin (mTOR), a phosphoinositide 3-kinase-related protein kinase, controls cell growth in response to nutrients and growth factors and is frequently deregulated in cancer. Here we report co-crystal structures of a complex of truncated mTOR and mammalian lethal with SEC13 protein 8 (mLST8) with an ATP transition state mimic and with ATP-site inhibitors ...

    The mammalian target of rapamycin (mTOR), a phosphoinositide 3-kinase-related protein kinase, controls cell growth in response to nutrients and growth factors and is frequently deregulated in cancer. Here we report co-crystal structures of a complex of truncated mTOR and mammalian lethal with SEC13 protein 8 (mLST8) with an ATP transition state mimic and with ATP-site inhibitors. The structures reveal an intrinsically active kinase conformation, with catalytic residues and a catalytic mechanism remarkably similar to canonical protein kinases. The active site is highly recessed owing to the FKBP12-rapamycin-binding (FRB) domain and an inhibitory helix protruding from the catalytic cleft. mTOR-activating mutations map to the structural framework that holds these elements in place, indicating that the kinase is controlled by restricted access. In vitro biochemistry shows that the FRB domain acts as a gatekeeper, with its rapamycin-binding site interacting with substrates to grant them access to the restricted active site. Rapamycin-FKBP12 inhibits the kinase by directly blocking substrate recruitment and by further restricting active-site access. The structures also reveal active-site residues and conformational changes that underlie inhibitor potency and specificity.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase mTORC [auth A], A [auth B]1174Homo 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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Target of rapamycin complex subunit LST8D [auth C], B [auth D]326Homo sapiensMutation(s): 0 
Gene Names: GBLLST8MLST8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BVC4 (Homo sapiens)
Explore Q9BVC4 
Go to UniProtKB:  Q9BVC4
PHAROS:  Q9BVC4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P2X (Subject of Investigation/LOI)
Query on P2X

Download Ideal Coordinates CCD File 
E [auth B], F [auth A]2-[4-amino-1-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-3-yl]-1H-indol-5-ol
C16 H16 N6 O
MFAQYJIYDMLAIM-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
P2XIC50:  3600   nM  BindingDB
P2XIC50:  3400   nM  BindingDB
P2XIC50:  8   nM  BindingDB
P2XIC50:  2000   nM  BindingDB
P2XKd:  3   nM  BindingDB
P2XIC50:  2200   nM  BindingDB
P2XIC50:  1500   nM  BindingDB
P2XIC50:  50   nM  BindingDB
P2XIC50:  1400   nM  BindingDB
P2XIC50:  410   nM  BindingDB
P2XIC50:  100   nM  BindingDB
P2XIC50:  1300   nM  BindingDB
P2XIC50:  5100   nM  BindingDB
P2XIC50:  1200   nM  BindingDB
P2XIC50:  4400   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.4α = 90
b = 163.2β = 90
c = 207.8γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2013-05-29
    Changes: Database references