9PCA | pdb_00009pca

HUMAN PRMT5:MEP50 COMPLEX IN COMPLEX WITH LIGAND 18


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.266 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Discovery of Gut-Restricted PRMT5 Inhibitors to Intercept Colorectal Cancer in Patients with Genetic Loss of Tumor Suppressor Adenomatous Polyposis Coli.

Hulpia, F.Schepens, W.Lepri, S.Nicolai, J.Jiang, Z.Boj, S.F.Bush, T.L.Carvalho, M.A.Chen, F.Chu, G.Clancy, K.W.Etwebi, Z.Everaerts, M.Fan, Y.Fernandez Candelaria, F.O.Francis, A.Hixon, M.S.Jardi, F.Jin, S.Larin, E.M.Last, S.Leenaerts, J.E.Li, S.Liddane, A.G.Lutter, F.H.Lv, D.Mattson, B.Milligan, C.M.Patrick, A.N.Patwardhan, G.A.Perez-Benito, L.Pieters, S.Renders, E.Retzbach, E.Smith-Monroy, C.Silva, J.Silva, M.Sterckx, H.Ten Hag, G.Thate, C.Van Brandt, S.Verissimo, C.S.Verniest, G.Vesely, E.Vetrano, I.Vinken, P.Wang, Y.Wong, V.Yao, X.Yang, J.Zijlmans, R.Bachman, K.E.Pocalyko, D.Jimenez, J.M.Gaffney, D.Thuring, J.W.

(2025) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00830
  • Primary Citation of Related Structures:  
    9PCA

  • PubMed Abstract: 

    Loss of the functional Adenomatous Polyposis Coli ( APC -LOF) tumor suppressor gene represents the disease-initiating event in most colorectal cancer (CRC) cases. A newly identified dependency between PRMT5 and APC -LOF suggests that inhibiting PRMT5 may help intercept CRC. To circumvent hematological toxicities associated with orally bioavailable first-generation PRMT5 inhibitors, we aimed to limit systemic exposure after oral administration. We describe our efforts, challenges, and compound evaluation workflow resulting in gut-restricted PRMT5 inhibitors. A two-pronged approach was envisioned, consisting of (1) minimizing passive absorption, and (2) maximizing systemic clearance by incorporation of a metabolic "soft spot". This resulted in 9 and 18 , displaying low absorption in preclinical species and high first-pass extraction mediated by aldehyde oxidase. 9 and 18 demonstrated in vivo colon pharmacodynamics without signs of systemic on-target toxicity, confirming gut-restriction. Administering 9 to dextran sodium sulfate (DSS)-treated polyp-bearing Apc Min/+ mice significantly reduced polyp number, indicating local treatment efficacy.


  • Organizational Affiliation
    • Global Discovery Chemistry, Therapeutics Discovery (TD), DPDS, Janssen Pharmaceutica NV, Johnson & Johnson Innovative Medicine, Beerse B-2340, Belgium.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein arginine N-methyltransferase 5645Homo sapiensMutation(s): 0 
Gene Names: PRMT5HRMT1L5IBP72JBP1SKB1
EC: 2.1.1.320
UniProt & NIH Common Fund Data Resources
Find proteins for O14744 (Homo sapiens)
Explore O14744 
Go to UniProtKB:  O14744
PHAROS:  O14744
GTEx:  ENSG00000100462 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14744
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Methylosome protein WDR77348Homo sapiensMutation(s): 0 
Gene Names: WDR77MEP50WD45HKMT1069Nbla10071
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQA1 (Homo sapiens)
Explore Q9BQA1 
Go to UniProtKB:  Q9BQA1
PHAROS:  Q9BQA1
GTEx:  ENSG00000116455 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BQA1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CHO (Subject of Investigation/LOI)
Query on A1CHO

Download Ideal Coordinates CCD File 
C [auth A](1S,2R,3S,5R)-3-{2-[2-amino-6-(2-hydroxyethyl)quinolin-7-yl]ethyl}-5-(7H-pyrrolo[2,3-d]pyrimidin-7-yl)cyclopentane-1,2-diol
C24 H27 N5 O3
XZLOKSDJSHSIIA-ZECSIRQKSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.266 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.807α = 90
b = 139.139β = 90
c = 179.354γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-09-10 
  • Deposition Author(s): Milligan, C.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release