SMTL ID : 8pkv.2 (1 other biounit)

Kelch domain of KEAP1 in complex with a ortho-dimethylbenzene linked cyclic peptide 4 (ortho-WRCDEETGEC).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-1-1-mer

Ligands

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

SO4.1: 1 residues within 4Å: Chain A: R.245 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.224, A:R.245, A:R.245 Salt bridges: A:R.245 SO4.2: 2 residues within 4Å: Chain A: N.130, R.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.130 Salt bridges: A:R.151

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

NA.3: 1 residues within 4Å: Chain A: C.126 No protein-ligand interaction detected (PLIP) NA.4: 5 residues within 4Å: Chain A: L.57, A.58, V.296, G.297 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.57 Water bridges: A:I.251

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

EDO.5: 3 residues within 4Å: Chain A: L.160, N.161, R.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.161, A:R.162 EDO.6: 2 residues within 4Å: Chain A: D.218, Q.220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.220 EDO.8: 5 residues within 4Å: Chain A: I.127, H.129, N.130, S.131, R.151 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.129, A:N.130, A:N.130, A:S.131, A:R.151 Water bridges: A:S.131

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: A.58, G.59, V.110, G.250, I.251, G.297, V.298 Ligands: NA.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.59, A:V.110, A:I.251, A:I.251, A:V.298 Water bridges: A:V.110 GOL.9: 3 residues within 4Å: Chain A: D.171, T.173, N.174 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.174 Water bridges: A:D.171

1 x ZK2: (2-methylphenyl)methanol(Covalent)

ZK2.10: 4 residues within 4Å: Chain B: R.3, C.4, G.9, C.11 No protein-ligand interaction detected (PLIP)

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
CP5: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
P

Kelch-like ECH-associated protein 1

CP5

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