6G3P | pdb_00006g3p

X-ray structure of seleno-methionine labelled NSD3-PWWP1

• PDB DOI: https://doi.org/10.2210/pdb6G3P/pdb

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


• Deposited: 2018-03-26 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: 2.80 Å
• R-Value Free: 
  0.262 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

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 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. [e-mail].
Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.
Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria.
Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany.
Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.
Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
Structural Genomics Consortium, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 72.28 kDa 
• Atom Count: 4,067 
• Modeled Residue Count: 473 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase NSD3	A, B, C, D	153	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 GTEx:  ENSG00000147548

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.262 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.04	α = 90
b = 88.55	β = 90.08
c = 77.97	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
SOLVE	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction

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
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Structure summary