6NM4

Crystal structure of SAM-bound PRDM9 in complex with MRK-740 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of a chemical probe for PRDM9.

Allali-Hassani, A.Szewczyk, M.M.Ivanochko, D.Organ, S.L.Bok, J.Ho, J.S.Y.Gay, F.P.H.Li, F.Blazer, L.Eram, M.S.Halabelian, L.Dilworth, D.Luciani, G.M.Lima-Fernandes, E.Wu, Q.Loppnau, P.Palmer, N.Talib, S.Z.A.Brown, P.J.Schapira, M.Kaldis, P.O'Hagan, R.C.Guccione, E.Barsyte-Lovejoy, D.Arrowsmith, C.H.Sanders, J.M.Kattar, S.D.Bennett, D.J.Nicholson, B.Vedadi, M.

(2019) Nat Commun 10: 5759-5759

  • DOI: 10.1038/s41467-019-13652-x
  • Primary Citation of Related Structures:  
    6NM4

  • PubMed Abstract: 
  • PRDM9 is a PR domain containing protein which trimethylates histone 3 on lysine 4 and 36. Its normal expression is restricted to germ cells and attenuation of its activity results in altered meiotic gene transcription, impairment of double-stranded breaks and pairing between homologous chromosomes ...

    PRDM9 is a PR domain containing protein which trimethylates histone 3 on lysine 4 and 36. Its normal expression is restricted to germ cells and attenuation of its activity results in altered meiotic gene transcription, impairment of double-stranded breaks and pairing between homologous chromosomes. There is growing evidence for a role of aberrant expression of PRDM9 in oncogenesis and genome instability. Here we report the discovery of MRK-740, a potent (IC 50 : 80 ± 16 nM), selective and cell-active PRDM9 inhibitor (Chemical Probe). MRK-740 binds in the substrate-binding pocket, with unusually extensive interactions with the cofactor S-adenosylmethionine (SAM), conferring SAM-dependent substrate-competitive inhibition. In cells, MRK-740 specifically and directly inhibits H3K4 methylation at endogenous PRDM9 target loci, whereas the closely related inactive control compound, MRK-740-NC, does not. The discovery of MRK-740 as a chemical probe for the PRDM subfamily of methyltransferases highlights the potential for exploiting SAM in targeting SAM-dependent methyltransferases.


    Organizational Affiliation

    Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada. m.vedadi@utoronto.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase PRDM9A, B191Homo sapiensMutation(s): 0 
Gene Names: PRDM9PFM6
EC: 2.1.1.43 (PDB Primary Data), 2.1.1 (UniProt), 2.1.1.359 (UniProt), 2.1.1.354 (UniProt), 2.1.1.355 (UniProt), 2.1.1.362 (UniProt), 2.1.1.361 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQV7 (Homo sapiens)
Explore Q9NQV7 
Go to UniProtKB:  Q9NQV7
PHAROS:  Q9NQV7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KS7
Query on KS7

Download Ideal Coordinates CCD File 
E [auth A], J [auth B]4-[3-(3,5-dimethoxyphenyl)-1,2,4-oxadiazol-5-yl]-1-methyl-9-(2-methylpyridin-4-yl)-1,4,9-triazaspiro[5.5]undecane
C25 H32 N6 O3
NZYTZRHHBAJPKN-UHFFFAOYSA-N
 Ligand Interaction
SAM
Query on SAM

Download Ideal Coordinates CCD File 
D [auth A], I [auth B]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], H [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], K [auth B]UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.026α = 90
b = 74.8β = 90
c = 141.435γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references