9KN9 | pdb_00009kn9

NSD2-PWWP1 domain bound with compound 1.

• PDB DOI: https://doi.org/10.2210/pdb9KN9/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-18 Released: 2025-11-26 
• Deposition Author(s): Huang, Y., Li, Y., Min, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.275 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Fragment Screening of NSD2-PWWP1 Identifies a Covalent Allosteric Site to Disrupt Both Methyllysine and DNA Binding

Huang, Y., Li, Y., Ren, Y., Min, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 31.24 kDa 
• Atom Count: 2,135 
• Modeled Residue Count: 256 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase NSD2	A [auth B], B [auth A]	133	Homo sapiens	Mutation(s): 0  Gene Names: NSD2, KIAA1090, MMSET, TRX5, WHSC1 EC: 2.1.1.357
UniProt & NIH Common Fund Data Resources
Find proteins for O96028 (Homo sapiens) Explore O96028  Go to UniProtKB:  O96028
PHAROS:  O96028 GTEx:  ENSG00000109685

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	E [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
A1EF6 (Subject of Investigation/LOI)	D [auth B], G [auth A]	(Z)-N-methyl-3-sulfanyl-prop-2-enamide C4 H7 N O S BYVOHKLWUDZCNW-NSCUHMNNSA-N
SO4	C [auth B], F [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.275 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.34	α = 90
b = 66.015	β = 110.9
c = 48.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Huang, Y., Li, Y., Min, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release