SMTL ID : 9rti.1

Structure of WRN in complex with ATPgS and covalent ligand Compound 7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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, F.35, K.36, Q.39, T.59, G.60, Y.61, G.62, K.63, S.64, M.312, G.313, R.340, R.343 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:S.34, A:K.36, A:Q.39, A:G.62, A:K.63, A:S.64, A:G.313, A:R.343, A:R.343 Water bridges: A:S.34, A:K.36, A:K.36, A:Y.61, A:Y.61, A:K.63, A:K.63, A:L.65, A:Q.91, A:G.311, A:I.314, A:N.315, A:R.340 Salt bridges: A:K.63, A:K.63, A:R.343 pi-Stacking: A:H.32, A:H.32

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

DMS.2: 8 residues within 4Å: Chain A: D.217, R.218, L.221, L.223, Y.335, I.338, R.396, L.400 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.218 DMS.25: 7 residues within 4Å: Chain A: K.27, M.28, Y.29, F.30, G.31, S.98 Ligands: PEG.24 No protein-ligand interaction detected (PLIP)

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

EDO.3: 6 residues within 4Å: Chain A: Y.222, Q.347, S.349, K.420, R.426 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.420, A:R.426 EDO.4: 8 residues within 4Å: Chain A: E.250, R.320, Q.321, Q.347, S.348, S.349 Ligands: EDO.3, PEG.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.349 Water bridges: A:E.250 EDO.5: 8 residues within 4Å: Chain A: Y.256, C.257, P.258, H.324, Y.325, G.326, A.327, P.328 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.326 Water bridges: A:C.257 EDO.6: 4 residues within 4Å: Chain A: D.90, Q.94, H.293, N.315 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.90, A:H.293 EDO.7: 8 residues within 4Å: Chain A: Y.280, H.293, F.310, G.311, M.312, I.314 Ligands: EDO.13, MLT.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.280, A:G.311 Water bridges: A:R.289, A:M.312 EDO.8: 8 residues within 4Å: Chain A: G.60, R.218, N.220, G.339, A.341, G.342, R.343 Ligands: EDO.23 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.220, A:N.220, A:G.339 EDO.9: 5 residues within 4Å: Chain A: A.190, E.332, S.333, Q.336, K.378 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.332, A:K.378 Water bridges: A:E.337 EDO.11: 5 residues within 4Å: Chain A: Y.29, F.30, Q.68, L.95, S.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.68, A:S.98, A:S.98 EDO.12: 6 residues within 4Å: Chain A: P.83, T.128, P.129, E.130, S.169, K.172 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.130 EDO.13: 5 residues within 4Å: Chain A: L.84, L.87, A.309, M.312 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.309 Water bridges: A:S.86, A:R.289 EDO.17: 2 residues within 4Å: Chain A: K.118, Q.141 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.118, A:Q.141 EDO.18: 5 residues within 4Å: Chain A: R.363, L.379, M.382, A.383, E.386 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.363, A:R.363 EDO.19: 1 residues within 4Å: Chain A: K.121 No protein-ligand interaction detected (PLIP) EDO.22: 4 residues within 4Å: Chain A: Y.73, V.74, G.75 Ligands: PEG.16 No protein-ligand interaction detected (PLIP) EDO.23: 5 residues within 4Å: Chain A: G.342, R.343, D.344, G.345 Ligands: EDO.8 No protein-ligand interaction detected (PLIP)

1 x 01: ~{N}-[1-[(4-fluorophenyl)methyl]-7-methyl-indazol-3-yl]propanamide

01.10: 18 residues within 4Å: Chain A: V.56, M.57, A.58, A.190, 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 Ligands: 02.14 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.56, A:A.58, A:E.332, A:E.332, A:Y.335, A:Y.335, A:H.402, A:F.403, A:F.403 Hydrogen bonds: A:G.215, A:H.402 pi-Stacking: A:H.402, A:F.403

1 x 02: ~{N}-[1-[(4-fluorophenyl)methyl]-7-methyl-indazol-3-yl]prop-2-enamide

02.14: 20 residues within 4Å: Chain A: V.56, M.57, A.58, A.190, T.191, 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, E.404 Ligands: 01.10 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.56, A:E.332, A:E.332, A:Y.335, A:H.402, A:F.403 Hydrogen bonds: A:G.215 pi-Stacking: A:H.402, A:F.403

1 x MLT: D-MALATE(Non-covalent)

MLT.15: 8 residues within 4Å: Chain A: S.86, L.87, D.90, F.286, K.290, H.293, H.294 Ligands: EDO.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.90, A:H.293 Water bridges: A:S.86, A:D.90, A:R.289 Salt bridges: A:K.290, A:H.293, A:H.294

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.16: 7 residues within 4Å: Chain A: Y.29, V.72, G.75, N.99, P.101, R.123 Ligands: EDO.22 No protein-ligand interaction detected (PLIP) PEG.20: 5 residues within 4Å: Chain A: E.250, R.320, L.346, Q.347 Ligands: EDO.4 No protein-ligand interaction detected (PLIP) PEG.21: 5 residues within 4Å: Chain A: L.47, R.50, V.74, K.76, T.149 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.76 PEG.24: 6 residues within 4Å: Chain A: M.28, Y.29, M.97, S.98, N.99 Ligands: DMS.25 No protein-ligand interaction detected (PLIP) PEG.26: 2 residues within 4Å: Chain A: R.298, E.300 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.27: 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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