6G24

X-ray structure of NSD3-PWWP1 in complex with compound 3

• PDB DOI:  https://doi.org/10.2210/pdb6G24/pdb

• Classification: ONCOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-03-22 Released: 2019-06-26 
• Deposition Author(s): Boettcher, J., Muellauer, B.J., Weiss-Puxbaum, A., Zoephel, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.235 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Literature

Fragment-based discovery of a chemical probe for the PWWP1 domain of NSD3.

Bottcher, J., Dilworth, D., Reiser, U., Neumuller, R.A., Schleicher, M., Petronczki, M., Zeeb, M., Mischerikow, N., Allali-Hassani, A., Szewczyk, M.M., Li, F., Kennedy, S., Vedadi, M., Barsyte-Lovejoy, D., Brown, P.J., Huber, K.V.M., Rogers, C.M., Wells, C.I., Fedorov, O., Rumpel, K., Zoephel, A., Mayer, M., Wunberg, T., Bose, D., Zahn, S., Arnhof, H., Berger, H., Reiser, C., Hormann, A., Krammer, T., Corcokovic, M., Sharps, B., Winkler, S., Haring, D., Cockcroft, X.L., Fuchs, J.E., Mullauer, B., Weiss-Puxbaum, A., Gerstberger, T., Boehmelt, G., Vakoc, C.R., Arrowsmith, C.H., Pearson, M., McConnell, D.B.

(2019) Nat Chem Biol 15: 822-829

• PubMed: 31285596 
• DOI: https://doi.org/10.1038/s41589-019-0310-x
• Primary Citation of Related Structures:  
  6G24, 6G25, 6G27, 6G29, 6G2B, 6G2C, 6G2E, 6G2F, 6G2O, 6G3P, 6G3T


• PubMed Abstract: 
  

Here, we report the fragment-based discovery of BI-9321, a potent, selective and cellular active antagonist of the NSD3-PWWP1 domain. The human NSD3 protein is encoded by the WHSC1L1 gene located in the 8p11-p12 amplicon, frequently amplified in breast and squamous lung cancer. Recently, it was demonstrated that the PWWP1 domain of NSD3 is required for the viability of acute myeloid leukemia cells. To further elucidate the relevance of NSD3 in cancer biology, we developed a chemical probe, BI-9321, targeting the methyl-lysine binding site of the PWWP1 domain with sub-micromolar in vitro activity and cellular target engagement at 1 µM. As a single agent, BI-9321 downregulates Myc messenger RNA expression and reduces proliferation in MOLM-13 cells. This first-in-class chemical probe BI-9321, together with the negative control BI-9466, will greatly facilitate the elucidation of the underexplored biological function of PWWP domains.

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Organizational Affiliation: 

Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 16.5 kDa 
• Atom Count: 1,134 
• Modelled Residue Count: 121 
• Deposited Residue Count: 136 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase NSD3	A	136	Homo sapiens	Mutation(s): 0  Gene Names: NSD3, WHSC1L1, DC28 EC: 2.1.1.43 (PDB Primary Data), 2.1.1.370 (UniProt), 2.1.1.371 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZ95 (Homo sapiens) Explore Q9BZ95  Go to UniProtKB:  Q9BZ95
PHAROS:  Q9BZ95

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EH2	B [auth A]	2-[(~{E})-2-thiophen-2-ylethenyl]benzoic acid C13 H10 O2 S ISSJZCAENPGUEW-BQYQJAHWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.235 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.213	α = 90
b = 46.741	β = 90
c = 63.754	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-26 
Deposition Author(s): Boettcher, J., Muellauer, B.J., Weiss-Puxbaum, A., Zoephel, A.

Revision History  

• Version 1.0: 2019-06-26
  Type: Initial release
  
• Version 1.1: 2020-01-15
  Changes: Database references