8VL7 | pdb_00008vl7

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

PDB DOI: https://doi.org/10.2210/pdb8VL7/pdb

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

Deposited: 2024-01-11 Released: 2024-01-24
Deposition Author(s): Dehghani-Tafti, S., Dong, A., Li, Y., Ackloo, S., Arrowsmith, C.H., Edwards, A.M., Halabelian, L.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.233 (Depositor), 0.237 (DCC)
R-Value Work:
0.192 (Depositor), 0.198 (DCC)
R-Value Observed:
0.194 (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.

To be published.

Macromolecule Content

Total Structure Weight: 204.85 kDa
Atom Count: 13,900
Modeled Residue Count: 1,763
Deposited Residue Count: 1,864
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, D, E A, B, C, D, E, F, G, H	233	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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1ACJ (Subject of Investigation/LOI) Query on A1ACJ Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain S [auth C] SDF format, chain O [auth B] SDF format, chain MA [auth H] SDF format, chain IA [auth G] SDF format, chain I [auth A] SDF format, chain EA [auth F] SDF format, chain AA [auth E] MOL2 format, chain X [auth D] MOL2 format, chain S [auth C] MOL2 format, chain O [auth B] MOL2 format, chain MA [auth H] MOL2 format, chain IA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain EA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain X [auth D] mmCIF format, chain S [auth C] mmCIF format, chain O [auth B] mmCIF format, chain MA [auth H] mmCIF format, chain IA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain EA [auth F] mmCIF format, chain AA [auth E]	AA [auth E] EA [auth F] I [auth A] IA [auth G] MA [auth H] AA [auth E], EA [auth F], I [auth A], IA [auth G], MA [auth H], O [auth B], S [auth C], X [auth D]	(2P)-2-[3-bromo-2-(2-hydroxyethoxy)phenyl]-5-hydroxy-1-methyl-N-(1,2-oxazol-4-yl)-6-oxo-1,6-dihydropyrimidine-4-carboxamide C₁₇ H₁₅ Br N₄ O₆ HNZOETDJOULZPF-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain EA [auth F] Focus chain I [auth A] Focus chain IA [auth G] Focus chain MA [auth H] Focus chain O [auth B] Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain EA [auth F] Focus chain I [auth A] Focus chain IA [auth G] Focus chain MA [auth H] Focus chain O [auth B] Focus chain S [auth C] Focus chain X [auth D]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain DA [auth E] MOL2 format, chain V [auth C] MOL2 format, chain DA [auth E] mmCIF format, chain V [auth C] mmCIF format, chain DA [auth E]	DA [auth E], V [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain V [auth C] Interactions & Density Focus chain DA [auth E] Focus chain V [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain W [auth C] MOL2 format, chain W [auth C] mmCIF format, chain W [auth C]	W [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain W [auth C] Interactions & Density Focus chain W [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain OA [auth H] SDF format, chain NA [auth H] SDF format, chain L [auth A] SDF format, chain KA [auth G] SDF format, chain K [auth A] SDF format, chain JA [auth G] SDF format, chain GA [auth F] SDF format, chain FA [auth F] SDF format, chain CA [auth E] SDF format, chain BA [auth E] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain OA [auth H] MOL2 format, chain NA [auth H] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth G] MOL2 format, chain GA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain CA [auth E] MOL2 format, chain BA [auth E] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain OA [auth H] mmCIF format, chain NA [auth H] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth G] mmCIF format, chain GA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain CA [auth E] mmCIF format, chain BA [auth E]	BA [auth E] CA [auth E] FA [auth F] GA [auth F] JA [auth G] BA [auth E], CA [auth E], FA [auth F], GA [auth F], JA [auth G], K [auth A], KA [auth G], L [auth A], NA [auth H], OA [auth H], P [auth B], Q [auth B], T [auth C], U [auth C], Y [auth D], Z [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain JA [auth G] Focus chain K [auth A] Focus chain KA [auth G] Focus chain L [auth A] Focus chain NA [auth H] Focus chain OA [auth H] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain JA [auth G] Focus chain K [auth A] Focus chain KA [auth G] Focus chain L [auth A] Focus chain NA [auth H] Focus chain OA [auth H] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain LA [auth G] SDF format, chain HA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth G] MOL2 format, chain HA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth G] mmCIF format, chain HA [auth F]	HA [auth F], LA [auth G], M [auth A], N [auth A], R [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain HA [auth F] Focus chain LA [auth G] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Interactions & Density Focus chain HA [auth F] Focus chain LA [auth G] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B]