9RPO | pdb_00009rpo

Crystal structure of DNPH1 bound by compound 3

PDB DOI: https://doi.org/10.2210/pdb9RPO/pdb

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

Deposited: 2025-06-25 Released: 2025-12-24
Deposition Author(s): Collie, G.W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.273 (Depositor), 0.267 (DCC)
R-Value Work:
0.247 (Depositor), 0.241 (DCC)
R-Value Observed:
0.248 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 35.1 kDa
Atom Count: 1,959
Modeled Residue Count: 235
Deposited Residue Count: 304
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43598
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JH5 (Subject of Investigation/LOI) Query on A1JH5 Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	1-[4-[[(2~{E})-2-(4-chloranylcyclohexa-2,4-dien-1-ylidene)-1,3-dihydroimidazol-4-yl]carbonyl]piperazin-1-yl]-2,2-dimethyl-propan-1-one C₁₉ H₂₅ Cl N₄ O₂ NKIIVXBCLGCNED-SSZFMOIBSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.273 (Depositor), 0.267 (DCC)
R-Value Work: 0.247 (Depositor), 0.241 (DCC)
R-Value Observed: 0.248 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.14	α = 90
b = 53.14	β = 90
c = 376.576	γ = 120

Software Package:

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

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-12-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.