SMTL ID : 8sge.1 (1 other biounit)

KLHDC2 Kelch Domain with ligand KDRLKZ-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

monomer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: A.37, H.271, S.272, H.322, T.323, A.324 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.37, A:H.271, A:A.324 Water bridges: A:A.37, A:L.273, A:L.273, A:L.273 GOL.2: 6 residues within 4Å: Chain A: S.39, D.40, C.98, V.99, D.100, R.101 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:C.98, A:D.100, A:D.100, A:R.101 Water bridges: A:D.100, A:D.100 GOL.3: 5 residues within 4Å: Chain A: V.266, T.288, T.289, D.290, Q.292 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.289, A:D.290, A:D.290 Water bridges: A:G.267, A:T.289, A:T.289, A:T.289, A:D.290, A:D.290, A:Q.292 GOL.4: 7 residues within 4Å: Chain A: I.263, C.264, P.265, V.266, D.296, W.298, Q.309 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.266, A:R.268, A:D.296, A:Q.309 Water bridges: A:Q.309 GOL.5: 3 residues within 4Å: Chain A: N.341, V.344, R.347 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.341, A:R.347, A:R.347 Water bridges: A:N.341

1 x ZWS: [(5P)-5-{3-[(2R)-butan-2-yl]-7-[(2-methoxyethoxy)carbonyl]-2-oxo-5,6,7,8-tetrahydro-1,7-naphthyridin-1(2H)-yl}-2-oxopyridin-1(2H)-yl]acetic acid(Non-covalent)

ZWS.6: 15 residues within 4Å: Chain A: Y.50, K.147, Y.163, W.191, A.219, A.220, R.236, R.241, S.269, W.270, K.291, W.321, L.342, L.343, H.345 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.321, A:L.342, A:L.343 Hydrogen bonds: A:R.236, A:R.241, A:S.269 Water bridges: A:K.147, A:R.236, A:K.291 Salt bridges: A:R.236, A:R.241 pi-Stacking: A:Y.163 pi-Cation interactions: A:K.147, A:R.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hickey, C.M. et al., Co-opting the E3 ligase KLHDC2 for targeted protein degradation by small molecules. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-01-03

Peptides

Kelch domain-containing protein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Kelch domain-containing protein 2

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