9S1O | pdb_00009s1o

Crystal structure of DNPH1 bound by compound 18

• PDB DOI: https://doi.org/10.2210/pdb9S1O/pdb

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


• Deposited: 2025-07-18 Released: 2025-12-24 
• Deposition Author(s): Collie, G.W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.258 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Discovery and Characterization of Diverse Non-nucleotide Inhibitors of DNPH1 Using an Integrated Hit Finding Strategy

Whitehurst, B.C., Anderson, N.A., Argyrou, A., Astles, P., Barlaam, B., Cadogan, E.B., Carlino, L., Collie, G.W., Edwards, A., Kitching, L., Li, Y., Milbradt, A.G., Nikkila, J., Northall, S., Pahlen, S., Patel, S., Savory, W., Schade, M., Spencer, J.A., Stead, D., Stubbs, C.J., Wang, A., Wang, W.

(2025) ACS Med Chem Lett 

• DOI: https://doi.org/10.1021/acsmedchemlett.5c00651

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.33 kDa 
• Atom Count: 2,120 
• Modeled Residue Count: 250 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-hydroxymethyl-dUMP N-hydrolase	A, B	152	Homo sapiens	Mutation(s): 0  Gene Names: DNPH1, C6orf108, RCL EC: 3.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for O43598 (Homo sapiens) Explore O43598  Go to UniProtKB:  O43598
PHAROS:  O43598 GTEx:  ENSG00000112667

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1JK6 (Subject of Investigation/LOI)	D [auth A], E [auth B]	2-[[2-[(1~{R},5~{S})-7-phenyl-3,7-diazabicyclo[3.3.1]nonan-3-yl]-1,3-thiazol-4-yl]methyl]-3,4-dihydro-1~{H}-isoquinoline-7-carboxylic acid C27 H30 N4 O2 S XGAITRPKSKWJAF-BGYRXZFFSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.258 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.345	α = 90
b = 149.345	β = 90
c = 53.965	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Collie, G.W.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release