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

Kelch domain of KEAP1 in complex with a ortho-dimethylbenzene linked cyclic peptide 5 (ortho-WRCDPETaEC).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

monomer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: S.55, R.72, N.74, N.106, R.107 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.55, A:N.74, A:N.74, A:N.106 Water bridges: A:R.107 Salt bridges: A:R.72, A:R.107 SO4.2: 1 residues within 4Å: Chain A: R.151 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.130 Salt bridges: A:R.151

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 1 residues within 4Å: Chain A: R.46 Ligand excluded by PLIP

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

EDO.4: 5 residues within 4Å: Chain A: Y.33, R.46, T.290, S.291, R.293 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.46, A:T.290, A:T.290, A:R.293 EDO.6: 2 residues within 4Å: Chain A: L.223, R.245 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.245, A:R.245 Water bridges: A:N.224, A:N.224

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: Q.220, D.221, Q.222 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.222 Water bridges: A:Y.217, A:Q.222, A:D.265

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

NA.7: 4 residues within 4Å: Chain A: S.200, G.201, Y.217, S.247 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.247, A:S.247 NA.8: 5 residues within 4Å: Chain A: R.228, D.230, T.235, W.236, T.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.230, A:T.235, A:T.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fonseca Lopez, F. et al., Computational Prediction of Cyclic Peptide Structural Ensembles and Application to the Design of Keap1 Binders. J.Chem.Inf.Model. (2023)

Release Date

2023-11-15

Peptides

Kelch-like ECH-associated protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Kelch-like ECH-associated protein 1

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