SMTL ID : 9rur.2 (1 other biounit)

Structure of WRN in complex with ATPgS and covalent ligand Compound 4d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 14 residues within 4Å: Chain A: H.32, S.34, F.35, K.36, Q.39, A.58, T.59, G.60, Y.61, G.62, K.63, S.64, R.343 Ligands: MG.9 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.34, A:K.36, A:Q.39, A:G.60, A:Y.61, A:G.62, A:K.63, A:S.64, A:S.64, A:S.64, A:R.343, A:R.343 Water bridges: A:E.155, A:N.315, A:R.340 Salt bridges: A:K.63 pi-Stacking: A:H.32, A:H.32

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

EDO.2: 6 residues within 4Å: Chain A: D.217, R.218, Y.335, I.338, I.399, L.400 No protein-ligand interaction detected (PLIP) EDO.5: 5 residues within 4Å: Chain A: K.329, D.330, K.378, M.381, M.382 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.329 EDO.6: 3 residues within 4Å: Chain A: R.260, G.283, M.284 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.260, A:R.260, A:G.283 Water bridges: A:H.281 EDO.7: 5 residues within 4Å: Chain A: L.87, G.311, M.312, N.315, R.340 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.311, A:R.340, A:R.340 Water bridges: A:R.343

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 5 residues within 4Å: Chain A: Y.222, S.349, H.351, R.426 Ligands: DMS.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.349 Water bridges: A:Y.222 DMS.4: 5 residues within 4Å: Chain A: R.226, P.238, F.239, H.351 Ligands: DMS.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.226, A:R.226 Salt bridges: A:E.250

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain A: C.394, C.421, C.422, C.425 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.394, A:C.421, A:C.422, A:C.425

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 3 residues within 4Å: Chain A: K.63, D.154 Ligands: AGS.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smith, G.M.T. et al., AI-assisted delivery of novel covalent WRN inhibitors from a non-covalent fragment screen. Bioorg.Med.Chem.Lett. (2025)

Release Date

2025-10-22

Peptides

Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN

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