SMTL ID : 9owd.1

Human WRN helicase in complex with allosteric ligand Compound 9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.409, C.436, C.437, C.440 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.409, A:C.436, A:C.437, A:C.440

1 x 01: N-[2-chloro-4-(trifluoromethyl)phenyl]-2-[(9R)-1'-(5-hydroxy-6-methylpyrimidine-4-carbonyl)-2-(morpholin-4-yl)-8-oxo-5,8-dihydrospiro[cyclopenta[d][1,2,4]triazolo[1,5-a]pyrimidine-7,4'-piperidin]-4(6H)-yl]acetamide

01.2: 22 residues within 4Å: Chain A: A.207, R.212, I.226, C.228, F.231, D.232, R.233, L.238, G.326, M.327, G.328, Y.350, Q.351, I.353, G.354, R.355, R.358, R.411, I.414, L.415, E.419 Ligands: EDO.5 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:R.233, A:Y.350, A:I.353, A:R.355, A:I.414, A:L.415 Hydrogen bonds: A:R.233, A:G.328, A:R.355, A:R.358, A:E.419 Water bridges: A:Y.350 pi-Cation interactions: A:R.233 Halogen bonds: A:Y.350, A:R.411, A:R.411

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

EDO.3: 7 residues within 4Å: Chain A: F.82, S.97, L.99, L.102, M.103, Q.106, D.169 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.97, A:S.97, A:Q.106, A:Q.106, A:D.169 EDO.4: 5 residues within 4Å: Chain A: Y.44, V.87, G.90, P.116, R.138 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.87, A:R.138 Water bridges: A:Y.44 EDO.5: 7 residues within 4Å: Chain A: V.71, A.207, S.208, R.212, I.226, R.358 Ligands: 01.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.212 Water bridges: A:A.207, A:R.212 EDO.6: 4 residues within 4Å: Chain A: R.241, P.253, F.254, H.366 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.241, A:R.241 EDO.7: 4 residues within 4Å: Chain A: G.189, R.217, C.218, N.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.189, A:N.220

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

DMS.8: 3 residues within 4Å: Chain A: D.131, K.136, Y.137 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, H. et al., High-throughput evaluation of novel WRN inhibitors. Slas Discov (2025)

Release Date

2025-09-10

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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