SMTL ID : 9o0x.2 (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: 19 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, N.121, Y.125, D.126, L.129, M.228 Ligands: MG.2, UNX.9 15 PLIP interactions: 15 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:H.120, A:H.120, A:N.121, A:N.121, A:D.196 Halogen bonds: A:A.17 01.10: 19 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.11, UNX.13, UNX.15 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.17, B:L.20, 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 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.11: 4 residues within 4Å: Chain B: D.14, M.15, D.126 Ligands: 01.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.14, H2O.5, H2O.5, H2O.5

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

EDO.3: 4 residues within 4Å: Chain A: 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.12: 6 residues within 4Å: Chain A: E.194 Chain B: L.33, P.56, 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

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

UNX.4: 2 residues within 4Å: Chain A: P.21, R.124 No protein-ligand interaction detected (PLIP) UNX.5: 3 residues within 4Å: Chain A: G.19, L.20, S.74 No protein-ligand interaction detected (PLIP) UNX.6: 3 residues within 4Å: Chain A: N.102 Chain B: N.102, A.106 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: 1 residues within 4Å: Chain A: W.214 No protein-ligand interaction detected (PLIP) UNX.9: 1 residues within 4Å: Ligands: 01.1 No protein-ligand interaction detected (PLIP) UNX.13: 4 residues within 4Å: Chain B: G.19, L.20, S.74 Ligands: 01.10 No protein-ligand interaction detected (PLIP) UNX.14: 4 residues within 4Å: Chain A: P.57, R.58, V.59 Chain B: H.91 No protein-ligand interaction detected (PLIP) UNX.15: 1 residues within 4Å: Ligands: 01.10 No protein-ligand interaction detected (PLIP) UNX.16: 1 residues within 4Å: Chain B: G.70 No protein-ligand interaction detected (PLIP) UNX.17: 3 residues within 4Å: Chain B: V.149, D.150, W.214 No protein-ligand interaction detected (PLIP) UNX.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.19: 4 residues within 4Å: Chain A: H.91 Chain B: P.57, R.58, V.59 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
B

B
C

Three-prime repair exonuclease 1

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