9N3L | pdb_00009n3l

Co-crystal structure of PCNA bound to HSP90alpha inhibitor, SNX2112

• PDB DOI: https://doi.org/10.2210/pdb9N3L/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-01-31 Released: 2026-02-25 
• Deposition Author(s): Jossart, J.J., Perry, J.J.
• Funding Organization(s): Department of Defense (DOD, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Screening for novel chemical scaffolds targeting PCNA identifies the Hsp90alpha inhibitor SNX-2112

Jossart, J., Ma, N., Haratipour, P., Li, C.M., Jang, C., Gu, L., O'Brien, T.E., Vaidehi, N., Malkas, L.H., Hickey, R.J., Perry, J.J.P.

(2026) Curr Res Struct Biol 11: 100183

• DOI: https://doi.org/10.1016/j.crstbi.2026.100183

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.43 kDa 
• Atom Count: 2,042 
• Modeled Residue Count: 246 
• Deposited Residue Count: 261 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proliferating cell nuclear antigen	A	261	Homo sapiens	Mutation(s): 0  Gene Names: PCNA
UniProt & NIH Common Fund Data Resources
Find proteins for P12004 (Homo sapiens) Explore P12004  Go to UniProtKB:  P12004
PHAROS:  P12004 GTEx:  ENSG00000132646

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E0G (Subject of Investigation/LOI)	B [auth A]	4-[6,6-dimethyl-4-oxidanylidene-3-(trifluoromethyl)-5,7-dihydroindazol-1-yl]-2-[(4-oxidanylcyclohexyl)amino]benzamide C23 H27 F3 N4 O3 ZFVRYNYOPQZKDG-MQMHXKEQSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	C [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.093	α = 90
b = 141.093	β = 90
c = 141.093	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-25 
Deposition Author(s): Jossart, J.J., Perry, J.J.

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Funding Organization	Location	Grant Number
Department of Defense (DOD, United States)	United States	--

Revision History  

• Version 1.0: 2026-02-25
  Type: Initial release