9O0X | pdb_00009o0x

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

PDB DOI: https://doi.org/10.2210/pdb9O0X/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: 1.68 Å
R-Value Free:
0.239 (Depositor), 0.248 (DCC)
R-Value Work:
0.197 (Depositor), 0.215 (DCC)
R-Value Observed:
0.198 (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: 77.27 kDa
Atom Count: 5,306
Modeled Residue Count: 630
Deposited Residue Count: 702
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NSU2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1B7U (Subject of Investigation/LOI) Query on A1B7U Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain Z [auth C] SDF format, chain Q [auth B] MOL2 format, chain D [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain Q [auth B] mmCIF format, chain D [auth A] mmCIF format, chain Z [auth C] mmCIF format, chain Q [auth B]	D [auth A], Q [auth B], Z [auth C]	5-({N-[(2,3-dichlorophenyl)methyl]-3,5-difluorobenzamido}methyl)-3-(methylamino)pyridine-2-carboxylic acid C₂₂ H₁₇ Cl₂ F₂ N₃ O₃ OLFOLTQPVNEEKT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain Q [auth B] Focus chain Z [auth C] Interactions & Density Focus chain D [auth A] Focus chain Q [auth B] Focus chain Z [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain S [auth B] SDF format, chain G [auth A] SDF format, chain BA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain S [auth B] MOL2 format, chain G [auth A] MOL2 format, chain BA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain S [auth B] mmCIF format, chain G [auth A] mmCIF format, chain BA [auth C]	BA [auth C], F [auth A], G [auth A], S [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain S [auth B] Interactions & Density Focus chain BA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain S [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain E [auth A] SDF format, chain AA [auth C] MOL2 format, chain R [auth B] MOL2 format, chain E [auth A] MOL2 format, chain AA [auth C] mmCIF format, chain R [auth B] mmCIF format, chain E [auth A] mmCIF format, chain AA [auth C]	AA [auth C], E [auth A], R [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain E [auth A] Focus chain R [auth B] Interactions & Density Focus chain AA [auth C] Focus chain E [auth A] Focus chain R [auth B]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain M [auth A] SDF format, chain V [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain IA [auth C] SDF format, chain I [auth A] SDF format, chain HA [auth C] SDF format, chain H [auth A] SDF format, chain GA [auth C] SDF format, chain FA [auth C] SDF format, chain EA [auth C] SDF format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain V [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain V [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain DA [auth C]	CA [auth C] DA [auth C] EA [auth C] FA [auth C] GA [auth C] CA [auth C], DA [auth C], EA [auth C], FA [auth C], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]