8ERA

RMC-5552 in complex with mTORC1 and FKBP12


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery of RMC-5552, a Selective Bi-Steric Inhibitor of mTORC1, for the Treatment of mTORC1-Activated Tumors.

Burnett, G.L.Yang, Y.C.Aggen, J.B.Pitzen, J.Gliedt, M.K.Semko, C.M.Marquez, A.Evans, J.W.Wang, G.Won, W.S.Tomlinson, A.C.A.Kiss, G.Tzitzilonis, C.Thottumkara, A.P.Cregg, J.Mellem, K.T.Choi, J.S.Lee, J.C.Zhao, Y.Lee, B.J.Meyerowitz, J.G.Knox, J.E.Jiang, J.Wang, Z.Wildes, D.Wang, Z.Singh, M.Smith, J.A.M.Gill, A.L.

(2023) J Med Chem 66: 149-169

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01658
  • Primary Citation of Related Structures:  
    8ER6, 8ER7, 8ERA

  • PubMed Abstract: 

    Hyperactivation of mTOR kinase by mutations in the PI3K/mTOR pathway or by crosstalk with other mutant cancer drivers, such as RAS, is a feature of many tumors. Multiple allosteric inhibitors of mTORC1 and orthosteric dual inhibitors of mTORC1 and mTORC2 have been developed as anticancer drugs, but their clinical utility has been limited. To address these limitations, we have developed a novel class of "bi-steric inhibitors" that interact with both the orthosteric and the allosteric binding sites in order to deepen the inhibition of mTORC1 while also preserving selectivity for mTORC1 over mTORC2. In this report, we describe the discovery and preclinical profile of the development candidate RMC-5552 and the in vivo preclinical tool compound RMC-6272. We also present evidence that selective inhibition of mTORC1 in combination with covalent inhibition of KRAS G12C shows increased antitumor activity in a preclinical model of KRAS G12C mutant NSCLC that exhibits resistance to KRAS G12C inhibitor monotherapy.


  • Organizational Affiliation

    Revolution Medicines, Incorporated, Redwood City, California 94063, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase mTOR2,549Homo sapiensMutation(s): 0 
Gene Names: MTORFRAPFRAP1FRAP2RAFT1RAPT1
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
GTEx:  ENSG00000198793 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42345
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP1A108Homo sapiensMutation(s): 0 
Gene Names: FKBP1AFKBP1FKBP12
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62942 (Homo sapiens)
Explore P62942 
Go to UniProtKB:  P62942
PHAROS:  P62942
GTEx:  ENSG00000088832 
Entity Groups  
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UniProt GroupP62942
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Target of rapamycin complex subunit LST8326Homo sapiensMutation(s): 0 
Gene Names: MLST8GBLLST8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BVC4 (Homo sapiens)
Explore Q9BVC4 
Go to UniProtKB:  Q9BVC4
PHAROS:  Q9BVC4
GTEx:  ENSG00000167965 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BVC4
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Regulatory-associated protein of mTORD [auth Y]1,335Homo sapiensMutation(s): 0 
Gene Names: RPTORKIAA1303RAPTOR
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N122 (Homo sapiens)
Explore Q8N122 
Go to UniProtKB:  Q8N122
PHAROS:  Q8N122
GTEx:  ENSG00000141564 
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UniProt GroupQ8N122
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XYU (Subject of Investigation/LOI)
Query on XYU

Download Ideal Coordinates CCD File 
F [auth B](3S,5R,6R,7E,9R,10R,12R,14S,15E,17E,19E,21S,23S,26R,27R,30R,34aS)-5,9,27-trihydroxy-3-{(2R)-1-[(1S,3R,4R)-4-hydroxy-3-methoxycyclohexyl]propan-2-yl}-10,21-dimethoxy-6,8,12,14,20,26-hexamethyl-5,6,9,10,12,13,14,21,22,23,24,25,26,27,32,33,34,34a-octadecahydro-3H-23,27-epoxypyrido[2,1-c][1,4]oxazacyclohentriacontine-1,11,28,29(4H,31H)-tetrone
C51 H81 N O13
IONVFRIQYMBCJN-PBSUYJRDSA-N
XZ9 (Subject of Investigation/LOI)
Query on XZ9

Download Ideal Coordinates CCD File 
E [auth A]1-[6-{[(3M)-4-amino-3-(2-amino-1,3-benzoxazol-5-yl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]methyl}-3,4-dihydroisoquinolin-2(1H)-yl]-3-hydroxypropan-1-one
C25 H24 N8 O3
XZVYCZDBNLILPS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release
  • Version 1.1: 2023-01-25
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection