SMTL ID : 9rur.1 (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: 15 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, M.312, G.313, R.340, R.343 Ligands: ADP.7 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:K.36, A:Q.39, A:Q.39, A:G.62, A:K.63, A:K.63, A:S.64, A:G.313, A:R.343, A:R.343 Water bridges: A:K.36, A:K.36, A:Y.61, A:I.314, A:I.314 Salt bridges: A:K.63, A:K.63 pi-Cation interactions: A:H.32, A:H.32, A:K.36, A:K.36

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

DMS.2: 8 residues within 4Å: Chain A: D.217, R.218, L.223, Y.335, I.338, R.396, I.399, L.400 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.218 Salt bridges: A:D.217 DMS.3: 6 residues within 4Å: Chain A: Y.222, Q.347, S.349, K.420, R.426 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.426, A:R.426 Water bridges: A:S.349 DMS.8: 8 residues within 4Å: Chain A: L.87, Y.280, H.293, A.309, F.310, G.311, M.312, I.314 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.280, A:M.312 pi-Cation interactions: A:H.293

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

EDO.4: 6 residues within 4Å: Chain A: E.250, R.320, Q.347, S.348, S.349 Ligands: DMS.3 No protein-ligand interaction detected (PLIP) EDO.5: 3 residues within 4Å: Chain A: I.85, S.86, E.89 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.86, A:E.89, A:E.89 EDO.9: 8 residues within 4Å: Chain A: Y.256, C.257, P.258, H.324, Y.325, G.326, A.327, P.328 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.256 EDO.10: 7 residues within 4Å: Chain A: E.155, F.166, R.167, F.170, I.196, D.199, I.200 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.166, A:F.166

1 x 01: 2-ethylsulfanyl-~{N}-[1-[(4-fluorophenyl)methyl]indazol-3-yl]ethanamide

01.6: 16 residues within 4Å: Chain A: V.56, A.58, A.192, C.213, T.214, G.215, M.331, E.332, Y.335, Q.336, Y.377, M.381, I.399, H.402, F.403, Q.407 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.56, A:A.58, A:A.192, A:E.332, A:Y.335, A:Y.335, A:Y.335, A:H.402, A:F.403 Hydrogen bonds: A:G.215, A:Q.407 pi-Stacking: A:H.402, A:F.403

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

ADP.7: 12 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 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:S.34, A:Q.39, A:G.60, A:G.62, A:K.63, A:S.64, A:S.64, A:S.64 Water bridges: A:K.36, A:K.36, A:Y.61, A:Y.61, A:R.343 Salt bridges: A:K.63, A:K.63, A:R.343, A:R.343 pi-Stacking: A:H.32, A:H.32

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 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

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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