SMTL ID : 9o0y.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x 01: N-[(2,3-dichlorophenyl)methyl]-3,5-difluoro-N-[(pyridin-3-yl)methyl]benzamide

01.1: 18 residues within 4Å: Chain A: M.15, E.16, A.17, G.19, L.20, P.21, P.25, S.74, A.76, A.77, I.80, Y.125, D.126, L.129, M.228 Ligands: MG.2, EDO.3, UNX.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.17, A:L.20, A:I.80, A:Y.125, A:L.129 Hydrogen bonds: A:E.16, A:A.17 Water bridges: A:D.196, A:D.196 pi-Stacking: A:Y.125 Halogen bonds: A:A.17 01.6: 18 residues within 4Å: Chain B: M.15, E.16, A.17, G.19, L.20, P.21, P.25, S.74, A.76, A.77, I.80, Y.125, D.126, L.129, M.228 Ligands: MG.7, EDO.8, UNX.9 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.17, B:L.20, B:I.80, B:Y.125, B:L.129 Hydrogen bonds: B:A.17 pi-Stacking: B:Y.125 Halogen bonds: B:A.17

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.14, D.126 Ligands: 01.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.14, H2O.1, H2O.1, H2O.1, H2O.4 MG.7: 3 residues within 4Å: Chain B: D.14, D.126 Ligands: 01.6 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.14, H2O.8, H2O.8, H2O.8, H2O.11

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: H.120, N.121, Y.125, S.174, L.175 Ligands: 01.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.121, A:L.175 Water bridges: A:R.124, A:G.176 EDO.8: 6 residues within 4Å: Chain B: H.120, N.121, Y.125, S.174, L.175 Ligands: 01.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.121, B:L.175 Water bridges: B:R.124, B:G.176

4 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.4: 4 residues within 4Å: Chain A: G.19, L.20, S.74 Ligands: 01.1 No protein-ligand interaction detected (PLIP) UNX.5: 3 residues within 4Å: Chain A: S.74, P.75, A.76 No protein-ligand interaction detected (PLIP) UNX.9: 4 residues within 4Å: Chain B: G.19, L.20, S.74 Ligands: 01.6 No protein-ligand interaction detected (PLIP) UNX.10: 3 residues within 4Å: Chain B: S.74, P.75, A.76 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dehghani-Tafti, S. et al., Co-crystal structure of human TREX1 in complex with an inhibitor. To be published

Release Date

2025-05-21

Peptides

Three-prime repair exonuclease 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Three-prime repair exonuclease 1

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