PWWP1 domain of NSD2 in complex with MR837

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 

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This is version 1.2 of the entry. See complete history


Discovery of Small-Molecule Antagonists of the PWWP Domain of NSD2.

Ferreira de Freitas, R.Liu, Y.Szewczyk, M.M.Mehta, N.Li, F.McLeod, D.Zepeda-Velazquez, C.Dilworth, D.Hanley, R.P.Gibson, E.Brown, P.J.Al-Awar, R.James, L.I.Arrowsmith, C.H.Barsyte-Lovejoy, D.Min, J.Vedadi, M.Schapira, M.Allali-Hassani, A.

(2021) J Med Chem 64: 1584-1592

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01768
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Increased activity of the lysine methyltransferase NSD2 driven by translocation and activating mutations is associated with multiple myeloma and acute lymphoblastic leukemia, but no NSD2-targeting chemical probe has been reported to date. Here, we present the first antagonists that block the protein-protein interaction between the N-terminal PWWP domain of NSD2 and H3K36me2. Using virtual screening and experimental validation, we identified the small-molecule antagonist 3f , which binds to the NSD2-PWWP1 domain with a K d of 3.4 μM and abrogates histone H3K36me2 binding to the PWWP1 domain in cells. This study establishes an alternative approach to targeting NSD2 and provides a small-molecule antagonist that can be further optimized into a chemical probe to better understand the cellular function of this protein.

  • Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase NSD2
A, B, C, D, E
A, B, C, D, E, F, G, H
141Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O96028 (Homo sapiens)
Explore O96028 
Go to UniProtKB:  O96028
PHAROS:  O96028
GTEx:  ENSG00000109685 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO96028
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q5D (Subject of Investigation/LOI)
Query on Q5D

Download Ideal Coordinates CCD File 
EA [auth C]
I [auth A]
KA [auth D]
LB [auth H]
OA [auth E]
EA [auth C],
I [auth A],
KA [auth D],
LB [auth H],
OA [auth E],
S [auth B],
UA [auth F],
ZA [auth G]
C16 H14 N2 O S
Query on UNX

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth G]
BA [auth B]
BB [auth G]
CA [auth B]
AA [auth B],
AB [auth G],
BA [auth B],
BB [auth G],
CA [auth B],
CB [auth G],
DA [auth B],
DB [auth G],
EB [auth G],
FA [auth C],
FB [auth G],
GA [auth C],
GB [auth G],
HA [auth C],
HB [auth G],
IA [auth C],
IB [auth G],
J [auth A],
JA [auth C],
JB [auth G],
K [auth A],
KB [auth G],
L [auth A],
LA [auth D],
M [auth A],
MA [auth D],
MB [auth H],
N [auth A],
NA [auth D],
NB [auth H],
O [auth A],
OB [auth H],
P [auth A],
PA [auth E],
Q [auth A],
QA [auth E],
R [auth A],
RA [auth E],
SA [auth E],
T [auth B],
TA [auth E],
U [auth B],
V [auth B],
VA [auth F],
W [auth B],
WA [auth F],
X [auth B],
XA [auth F],
Y [auth B],
YA [auth F],
Z [auth B]
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.21α = 90
b = 70.32β = 90
c = 228.83γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2021-04-21
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description