SMTL ID : 7gqu.1

Crystal Structure of Werner helicase fragment 517-945 in covalent complex with N-[(E,1S)-1-cyclopropyl-3-methylsulfonylprop-2-enyl]-2-(1,1-difluoroethyl)-4-phenoxypyrimidine-5-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.393, C.420, C.421, C.424 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.393, A:C.420, A:C.421, A:C.424

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

ADP.2: 13 residues within 4Å: Chain A: H.31, S.33, F.34, K.35, Q.38, T.58, G.59, Y.60, G.61, K.62, S.63, R.342 Ligands: GOL.4 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:S.33, A:K.35, A:Q.38, A:A.57, A:G.59, A:Y.60, A:G.61, A:K.62, A:S.63, A:R.342 Water bridges: A:H.31, A:S.33, A:S.63, A:S.63, A:L.64, A:R.342, A:R.342 Salt bridges: A:R.342, A:R.342 pi-Stacking: A:H.31, A:H.31

1 x X1L: N-[(1S)-1-cyclopropyl-3-(methanesulfonyl)propyl]-2-(1,1-difluoroethyl)-4-phenoxypyrimidine-5-carboxamide(Covalent)

X1L.3: 16 residues within 4Å: Chain A: V.55, M.56, A.189, A.191, R.196, C.212, T.213, M.330, E.331, Y.334, M.380, K.383, H.401, F.402, E.403, K.405 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.55, A:A.191, A:Y.334, A:F.402 Hydrogen bonds: A:K.383 pi-Stacking: A:Y.334

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: F.29, G.30, H.31 Ligands: ADP.2, NA.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.30, A:H.31 Water bridges: A:G.30

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 2 residues within 4Å: Chain A: G.30 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.30, A:S.32, A:S.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baltgalvis, K.A. et al., Chemoproteomic discovery of a covalent allosteric inhibitor of WRN helicase. Nature (2024)

Release Date

2024-05-01

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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