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

Kelch domain of KEAP1 in complex with ortho-dimethylbenzene linked cyclic peptide 3 (ortho-WRCDEETGEC).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: I.127, H.129, N.130, S.131, R.151 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.130, A:S.131, A:S.131 Water bridges: A:H.129, A:H.129, A:R.151, A:R.151 Salt bridges: A:H.129, A:R.151 SO4.2: 3 residues within 4Å: Chain A: R.72, N.74, N.106 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.55, A:N.74, A:N.106 Salt bridges: A:R.72 SO4.3: 2 residues within 4Å: Chain A: R.46 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.46 SO4.4: 1 residues within 4Å: Chain A: R.151 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.130 Water bridges: A:R.151 Salt bridges: A:R.151

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

CL.5: 4 residues within 4Å: Chain A: A.58, G.59, G.297, V.298 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain A: N.224, R.245 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.224, A:R.245 GOL.9: 8 residues within 4Å: Chain A: G.56, R.107, I.108, G.154, G.201, A.202, A.248, G.295 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.108, A:G.154 Water bridges: A:R.107

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

EDO.7: 5 residues within 4Å: Chain A: Y.33, T.290, S.291, R.293 Ligands: SO4.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.290, A:T.290, A:R.293 Water bridges: A:R.46 EDO.8: 7 residues within 4Å: Chain A: G.17, R.18, N.38, P.39, S.40, H.254, Q.255 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.18, A:N.38, A:S.40 Water bridges: A:N.38, A:Q.255 EDO.10: 2 residues within 4Å: Chain A: H.143, L.144 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.144 Water bridges: A:S.102, A:W.142 EDO.11: 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 EDO.12: 3 residues within 4Å: Chain A: V.239, A.240, D.281 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.239, A:A.240

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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