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

Structure of WRN in complex with ATPgS and Compound 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

monomer

Ligands

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

AGS.1: 15 residues within 4Å: Chain A: H.32, S.34, K.36, Q.39, A.58, G.60, Y.61, G.62, K.63, S.64, N.315, R.340, R.343 Ligands: ADP.6, MG.9 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:S.34, A:K.36, A:Q.39, A:G.60, A:G.62, A:K.63, A:K.63, A:S.64, A:E.155, A:E.155, A:R.340, A:R.343, A:R.343 Water bridges: A:S.64, A:N.315, A:N.315 Salt bridges: A:K.63, A:R.343, A:R.343 pi-Stacking: A:H.32, A:H.32

1 x GQP: 1-[(4-fluorophenyl)methyl]benzimidazole(Covalent)

GQP.2: 11 residues within 4Å: Chain A: V.56, A.190, T.191, A.192, F.216, M.331, E.332, M.381, I.399, H.402, F.403 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.56, A:T.191, A:F.216, A:M.331, A:H.402, A:F.403, A:F.403, A:F.403 pi-Stacking: A:F.216

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

DMS.3: 6 residues within 4Å: Chain A: Y.222, Q.347, S.349, K.420, R.426 Ligands: DMS.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.426 Water bridges: A:S.349, A:R.426 DMS.4: 5 residues within 4Å: Chain A: R.320, Q.347, S.348, S.349 Ligands: DMS.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.250

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

EDO.5: 9 residues within 4Å: Chain A: Y.256, C.257, P.258, I.308, H.324, Y.325, G.326, A.327, P.328 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.258 EDO.7: 7 residues within 4Å: Chain A: F.216, D.217, R.218, L.223, Y.335, I.338, R.396 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.217, A:R.218

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.6: 13 residues within 4Å: Chain A: H.32, S.34, K.36, Q.39, T.59, G.60, Y.61, G.62, K.63, S.64, R.343 Ligands: AGS.1, MG.9 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.34, A:K.36, A:Q.39, A:A.58, A:G.60, A:G.62, A:K.63, A:S.64, A:S.64, A:S.64 Water bridges: A:L.65, A:L.65, A:Q.91 Salt bridges: A:K.63, A:R.343 pi-Stacking: A:H.32, A:H.32

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: 5 residues within 4Å: Chain A: K.63, D.154, E.155 Ligands: AGS.1, ADP.6 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
A

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

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