SMTL ID : 9o0w.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-dimer

Ligands

2 x 01: 5-({N-[(2,3-dichlorophenyl)methyl]-3,5-difluorobenzamido}methyl)pyridine-2-carboxylic acid

01.1: 18 residues within 4Å: Chain A: D.14, M.15, E.16, A.17, G.19, L.20, P.21, P.25, S.74, A.77, I.80, H.120, Y.125, D.126, L.129, M.228 Ligands: MG.2, UNX.8 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.17, A:L.20, A:I.80, A:I.80, A:Y.125, A:L.129 Hydrogen bonds: A:E.16, A:A.17 Water bridges: A:D.14, A:H.120 pi-Stacking: A:Y.125 Halogen bonds: A:A.17 01.9: 18 residues within 4Å: Chain B: D.14, M.15, E.16, A.17, G.19, L.20, P.21, P.25, S.74, A.77, I.80, H.120, Y.125, D.126, L.129, M.228 Ligands: MG.10, UNX.16 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.17, B:L.20, B:I.80, B:I.80, B:Y.125, B:L.129 Hydrogen bonds: B:A.17 Water bridges: B:H.120, B:D.196 pi-Stacking: B:Y.125 Halogen bonds: B:A.17

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.14 Ligands: 01.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.14, H2O.1, H2O.1, H2O.1 MG.10: 2 residues within 4Å: Chain B: D.14 Ligands: 01.9 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.14, H2O.8, H2O.9, H2O.9

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

EDO.3: 5 residues within 4Å: Chain A: L.33, V.60, K.62, L.198 Chain B: E.194 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.62 Water bridges: A:K.62, B:E.194 EDO.11: 5 residues within 4Å: Chain A: E.194 Chain B: L.33, V.60, K.62, L.198 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:E.194, B:K.62 Hydrogen bonds: B:K.62

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

UNX.4: 2 residues within 4Å: Chain A: L.20, S.22 No protein-ligand interaction detected (PLIP) UNX.5: 2 residues within 4Å: Chain A: P.21, R.124 No protein-ligand interaction detected (PLIP) UNX.6: 2 residues within 4Å: Chain A: P.75, A.76 No protein-ligand interaction detected (PLIP) UNX.7: 4 residues within 4Å: Chain A: R.207, P.208, Q.209, A.210 No protein-ligand interaction detected (PLIP) UNX.8: 4 residues within 4Å: Chain A: G.19, L.20, S.74 Ligands: 01.1 No protein-ligand interaction detected (PLIP) UNX.12: 2 residues within 4Å: Chain B: L.20, S.22 No protein-ligand interaction detected (PLIP) UNX.13: 2 residues within 4Å: Chain B: P.21, R.124 No protein-ligand interaction detected (PLIP) UNX.14: 2 residues within 4Å: Chain B: P.75, A.76 No protein-ligand interaction detected (PLIP) UNX.15: 4 residues within 4Å: Chain B: R.207, P.208, Q.209, A.210 No protein-ligand interaction detected (PLIP) UNX.16: 4 residues within 4Å: Chain B: G.19, L.20, S.74 Ligands: 01.9 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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