9DHK | pdb_00009dhk

RMI1-RMI2 bound to cyclic peptide L3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.247 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.204 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Potent Cyclic Peptide Inhibitors Disrupt the FANCM-RMI Interaction.

Alcock, L.J.Gao, T.Bythell-Douglas, R.Gao, J.Krishna Sudhakar, H.Huang, T.Young, R.Vu, Q.N.Deshpande, C.Wilkinson-White, L.E.Passioura, T.Pickett, H.A.Deans, A.J.Lau, Y.H.

(2025) J Med Chem 68: 12615-12625

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00365
  • Primary Citation of Related Structures:  
    9DHK, 9DI4

  • PubMed Abstract: 

    FANCM-RMI is a protein-protein interaction that maintains genome stability during DNA repair events in cancers that rely on the Alternative Lengthening of Telomeres (ALT) pathway for survival. We report the first valid chemical inhibitors of the FANCM-RMI interaction discovered by screening cyclic peptides via mRNA display. These inhibitors engage the FANCM-binding pocket of RMI1/2 with nanomolar affinity ( K D = 2-10 nM) and are potent disruptors of the FANCM-RMI interaction (IC 50 = 54-104 nM). X-ray crystallography and alanine scanning reveal novel binding modes and interactions between the cyclic peptides and RMI1/2 that drive high-potency inhibition. Co-immunoprecipitation studies confirm the complete disruption of the native interaction in whole osteosarcoma cell lysates. These inhibitors represent the first validated RMI binders toward developing chemical tools for interrogating the mechanistic roles of FANCM-RMI in mediating genome stability and provide a much-anticipated starting point to accelerate the development of FANCM-RMI inhibitors for intervention against ALT-driven cancers.


  • Organizational Affiliation

    School of Chemistry, The University of Sydney, Camperdown, NSW 2145, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RecQ-mediated genome instability protein 1A,
C [auth D],
G [auth J]
152Homo sapiensMutation(s): 0 
Gene Names: RMI1C9orf76
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9A7 (Homo sapiens)
Explore Q9H9A7 
Go to UniProtKB:  Q9H9A7
PHAROS:  Q9H9A7
GTEx:  ENSG00000178966 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H9A7
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RecQ-mediated genome instability protein 2B,
H [auth K]
147Homo sapiensMutation(s): 0 
Gene Names: RMI2C16orf75
UniProt & NIH Common Fund Data Resources
Find proteins for Q96E14 (Homo sapiens)
Explore Q96E14 
Go to UniProtKB:  Q96E14
PHAROS:  Q96E14
GTEx:  ENSG00000175643 
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UniProt GroupQ96E14
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RecQ-mediated genome instability protein 2D [auth E]135Homo sapiensMutation(s): 0 
Gene Names: RMI2C16orf75
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Find proteins for Q96E14 (Homo sapiens)
Explore Q96E14 
Go to UniProtKB:  Q96E14
PHAROS:  Q96E14
GTEx:  ENSG00000175643 
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UniProt GroupQ96E14
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RecQ-mediated genome instability protein 1E [auth G]145Homo sapiensMutation(s): 0 
Gene Names: RMI1C9orf76
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Find proteins for Q9H9A7 (Homo sapiens)
Explore Q9H9A7 
Go to UniProtKB:  Q9H9A7
PHAROS:  Q9H9A7
GTEx:  ENSG00000178966 
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UniProt GroupQ9H9A7
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RecQ-mediated genome instability protein 2F [auth H]139Homo sapiensMutation(s): 0 
Gene Names: RMI2C16orf75
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Find proteins for Q96E14 (Homo sapiens)
Explore Q96E14 
Go to UniProtKB:  Q96E14
PHAROS:  Q96E14
GTEx:  ENSG00000175643 
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  • Reference Sequence

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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
L3 peptideI [auth C],
J [auth F],
K [auth I],
L
15synthetic constructMutation(s): 0 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.247 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.204 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.15α = 90
b = 50.622β = 118.047
c = 181.221γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP2003250
National Health and Medical Research Council (NHMRC, Australia)AustraliaMRF2007488

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2025-07-09
    Changes: Database references