SMTL ID : 9o0x.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-dimer

Ligands

2 x 01: 5-({N-[(2,3-dichlorophenyl)methyl]-3,5-difluorobenzamido}methyl)-3-(methylamino)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.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.17, A:I.80, A:Y.125, A:Y.125, A:Y.125, A:Y.125, A:L.129 Hydrogen bonds: A:E.16, A:A.17 Water bridges: A:D.14, A:D.14, A:H.120 Halogen bonds: A:A.17 01.14: 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.15, UNX.18 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.17, B:I.80, B:Y.125, B:Y.125, B:Y.125, B:Y.125, B:L.129 Hydrogen bonds: B:A.17 Water bridges: B:H.120, B:D.196 Halogen bonds: B:A.17

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.14, M.15, D.126 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.15: 4 residues within 4Å: Chain B: D.14, M.15, D.126 Ligands: 01.14 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.14, H2O.5, H2O.6, H2O.6

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

EDO.3: 5 residues within 4Å: Chain A: A.39, P.57, R.58, V.59 Chain B: H.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.58, A:V.59 EDO.4: 4 residues within 4Å: Chain A: V.60, K.62, L.198 Chain B: E.194 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:E.194 Hydrogen bonds: A:K.62 EDO.16: 5 residues within 4Å: Chain A: H.91 Chain B: A.39, P.57, R.58, V.59 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.58, B:V.59 EDO.17: 4 residues within 4Å: Chain A: E.194 Chain B: V.60, K.62, L.198 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:E.194, A:E.194 Hydrogen bonds: B:K.62

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

UNX.5: 4 residues within 4Å: Chain A: G.19, L.20, S.74 Ligands: 01.1 Ligand excluded by PLIP UNX.6: 1 residues within 4Å: Chain A: A.76 Ligand excluded by PLIP UNX.7: 1 residues within 4Å: Chain A: T.85 Ligand excluded by PLIP UNX.8: 2 residues within 4Å: Chain A: P.21, R.124 Ligand excluded by PLIP UNX.9: 4 residues within 4Å: Chain A: L.139, T.140, S.141, A.142 Ligand excluded by PLIP UNX.10: 4 residues within 4Å: Chain A: R.207, P.208, Q.209, A.210 Ligand excluded by PLIP UNX.11: 1 residues within 4Å: Chain A: W.214 Ligand excluded by PLIP UNX.12: 3 residues within 4Å: Chain A: D.150, W.214, R.220 Ligand excluded by PLIP UNX.13: 3 residues within 4Å: Chain A: N.102 Chain B: N.102 Ligands: UNX.26 Ligand excluded by PLIP UNX.18: 4 residues within 4Å: Chain B: G.19, L.20, S.74 Ligands: 01.14 Ligand excluded by PLIP UNX.19: 1 residues within 4Å: Chain B: A.76 Ligand excluded by PLIP UNX.20: 1 residues within 4Å: Chain B: T.85 Ligand excluded by PLIP UNX.21: 2 residues within 4Å: Chain B: P.21, R.124 Ligand excluded by PLIP UNX.22: 4 residues within 4Å: Chain B: L.139, T.140, S.141, A.142 Ligand excluded by PLIP UNX.23: 4 residues within 4Å: Chain B: R.207, P.208, Q.209, A.210 Ligand excluded by PLIP UNX.24: 1 residues within 4Å: Chain B: W.214 Ligand excluded by PLIP UNX.25: 3 residues within 4Å: Chain B: D.150, W.214, R.220 Ligand excluded by PLIP UNX.26: 3 residues within 4Å: Chain A: N.102 Chain B: N.102 Ligands: UNX.13 Ligand excluded by 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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