8Q69 | pdb_00008q69

Crystal structure of HsRNMT complexed with inhibitor DDD1060606


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 
    0.289 (Depositor), 0.283 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

Starting Model: experimental
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Literature

Characterisation of RNA guanine-7 methyltransferase (RNMT) using a small molecule approach.

Pearson, L.A.Petit, A.P.Mendoza Martinez, C.Bellany, F.Lin, D.Niven, S.Swift, R.Eadsforth, T.Fyfe, P.Paul, M.Postis, V.Hu, X.Cowling, V.H.Gray, D.W.

(2025) Biochem J 482

  • DOI: https://doi.org/10.1042/BCJ20240608
  • Primary Citation of Related Structures:  
    8Q69, 8Q8G, 8Q9W

  • PubMed Abstract: 

    The maturation of the RNA cap involving guanosine N-7 methylation, catalyzsed by the HsRNMT (RNA guanine-7 methyltransferase (HsRNMT)-RAM (RNA guanine-N7 methyltransferase activating subunit (RAM) complex, is currently under investigation as a novel strategy to combat PIK3CA -mutant breast cancer. However, the development of effective drugs is hindered by a limited understanding of the enzyme's mechanism and a lack of small molecule inhibitors. Following the elucidation of the HsRNMT-RAM molecular mechanism, we report the biophysical characterizsation of two small molecule hits. Biophysics, biochemistry and structural biology confirm that both compounds bind competitively with cap and bind effectively to HsRNMT-RAM in the presence of the co-product SAH, with a binding affinity (KD) of approximately 1 μM. This stabilisation of the enzyme--product complex results in uncompetitive inhibition. Finally, we describe the properties of the cap pocket and provided suggestions for further development of the tool compounds.


  • Organizational Affiliation
    • Drug Discovery Unit, School of Life Sciences, University of Dundee, Dundee, U.K.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA cap guanine-N7 methyltransferase
A, B
276Homo sapiensMutation(s): 0 
Gene Names: RNMTKIAA0398
EC: 2.1.1.56
UniProt & NIH Common Fund Data Resources
Find proteins for O43148 (Homo sapiens)
Explore O43148 
Go to UniProtKB:  O43148
PHAROS:  O43148
GTEx:  ENSG00000101654 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43148
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
K7R (Subject of Investigation/LOI)
Query on K7R

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
1-[(3~{S})-3-(2~{H}-pyrazolo[3,4-b]pyridin-3-yl)piperidin-1-yl]-2-thiophen-3-yl-ethanone
C17 H18 N4 O S
YFQQTIRINPYCBC-ZDUSSCGKSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free:  0.289 (Depositor), 0.283 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.195α = 90
b = 84.574β = 99.03
c = 81.966γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-21
    Type: Initial release
  • Version 1.1: 2025-03-12
    Changes: Data collection, Database references, Structure summary