9O0Y | pdb_00009o0y

Co-crystal structure of human TREX1 in complex with an inhibitor

PDB DOI: https://doi.org/10.2210/pdb9O0Y/pdb

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

Deposited: 2025-04-03 Released: 2025-05-21
Deposition Author(s): Dehghani-Tafti, S., Dong, A., Li, Y., Ackloo, S., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.168 (Depositor), 0.180 (DCC)
R-Value Work:
0.143 (Depositor), 0.163 (DCC)
R-Value Observed:
0.143 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Co-crystal structure of human TREX1 in complex with an inhibitor

Dehghani-Tafti, S., Dong, A., Li, Y., Ackloo, S., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 77.05 kDa
Atom Count: 5,670
Modeled Residue Count: 647
Deposited Residue Count: 702
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Three-prime repair exonuclease 1	A, B, C	234	Homo sapiens	Mutation(s): 0 Gene Names: TREX1 EC: 3.1.11.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NSU2 (Homo sapiens) Explore Q9NSU2 Go to UniProtKB: Q9NSU2
PHAROS: Q9NSU2 GTEx: ENSG00000213689
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NSU2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1B7T (Subject of Investigation/LOI) Query on A1B7T Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] SDF format, chain N [auth C] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain N [auth C]	D [auth A], I [auth B], N [auth C]	N-[(2,3-dichlorophenyl)methyl]-3,5-difluoro-N-[(pyridin-3-yl)methyl]benzamide C₂₀ H₁₄ Cl₂ F₂ N₂ O RDIHBIADEXQZSH-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain N [auth C] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain N [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C]	F [auth A], K [auth B], P [auth C], Q [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain Q [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C]	E [auth A], J [auth B], O [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C]	G [auth A] H [auth A] L [auth B] M [auth B] R [auth C] G [auth A], H [auth A], L [auth B], M [auth B], R [auth C], S [auth C]	UNKNOWN ATOM OR ION X		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C]