9KNB | pdb_00009knb

NSD2-PWWP1 domain bound with compound 9

• PDB DOI: https://doi.org/10.2210/pdb9KNB/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: 1.84 Å
• R-Value Free: 
  0.275 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.236 (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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.79 kDa 
• Atom Count: 1,080 
• Modeled Residue Count: 125 
• Deposited Residue Count: 133 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase NSD2	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EF7 (Subject of Investigation/LOI)	C [auth A]	N-(2-methoxyphenyl)-2-selanyl-benzamide C14 H13 N O2 Se DGVCWDGVOWMWNP-UHFFFAOYSA-N
EPE	B [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.275 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.731	α = 90
b = 55.731	β = 90
c = 40.448	γ = 120

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