9YSP | pdb_00009ysp

Human DCTPP1 bound to a Class III inhibitor

PDB DOI: https://doi.org/10.2210/pdb9YSP/pdb

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

Deposited: 2025-10-19 Released: 2026-06-10
Deposition Author(s): Hauk, G., Berger, J.M.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.191 (Depositor), 0.190 (DCC)
R-Value Work:
0.165 (Depositor), 0.167 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9YSP

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

Literature

Structural insights into novel DCTPP1 antagonists and their synergistic action with DNMT inhibitors

Hauk, G., Liu, J., Nelson, W.G., Yegnasubramanian, S., Berger, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 52.4 kDa
Atom Count: 3,852
Modeled Residue Count: 425
Deposited Residue Count: 440
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dCTP pyrophosphatase 1	A, B, C, D	110	Homo sapiens	Mutation(s): 0 Gene Names: DCTPP1, XTP3TPA, CDA03 EC: 3.6.1.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H773 (Homo sapiens) Explore Q9H773 Go to UniProtKB: Q9H773
PHAROS: Q9H773 GTEx: ENSG00000179958
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H773
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1C0C( Subject of Investigation/LOI) Query on A1C0C Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	4-(4-chlorophenyl)-6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-(methylsulfanyl)pyrimidine-5-carbonitrile C₁₈ H₂₀ Cl N₅ O S UVSXTOAXDVXKRJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.191 (Depositor), 0.190 (DCC)
R-Value Work: 0.165 (Depositor), 0.167 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.959	α = 90
b = 80.964	β = 90
c = 99.79	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Coot	model building
PHASER	phasing
Aimless	data scaling

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-10

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R35-CA263778

Revision History (Full details and data files)

Version 1.0: 2026-06-10
Type: Initial release

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.