SMTL ID : 8xgv.1

Optimization Efforts for Identification of Novel Highly Potent Keap1-Nrf2 Protein-Protein Interaction (PPI) Inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

monomer

Ligands

1 x 01: (2~{R},3~{S})-3-[[(2~{S})-2-[4-[(3-ethoxypyridin-2-yl)methyl]phenyl]-2-fluoranyl-ethanoyl]amino]-2-methyl-3-(4-methylphenyl)propanoic acid

01.1: 15 residues within 4Å: Chain A: Y.25, R.106, I.152, G.153, F.169, R.174, S.199, G.200, Y.216, Q.221, S.246, A.247, Y.263, F.268, S.293 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:R.106, A:I.152, A:F.169, A:A.247, A:A.247, A:Y.263, A:Y.263, A:F.268 Hydrogen bonds: A:R.106, A:S.199, A:S.199, A:S.246 Water bridges: A:R.106 Salt bridges: A:R.174 pi-Stacking: A:Y.25 pi-Cation interactions: A:R.106

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 6 residues within 4Å: Chain A: I.112, D.113, H.115, Y.117, R.133, P.183 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.112, A:P.183 Hydrogen bonds: A:D.113 Salt bridges: A:H.115, A:R.133

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

SO4.3: 1 residues within 4Å: Chain A: R.185 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.185 SO4.4: 4 residues within 4Å: Chain A: C.125, I.126, H.127, R.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.127 Salt bridges: A:H.127, A:R.150 SO4.5: 3 residues within 4Å: Chain A: W.141, H.142, L.143 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.143 Water bridges: A:W.141 Salt bridges: A:H.142 SO4.6: 5 residues within 4Å: Chain A: H.115, E.135, P.136, E.137, R.138 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.137, A:R.138 Water bridges: A:E.137, A:R.138 Salt bridges: A:H.115, A:R.138 SO4.7: 2 residues within 4Å: Chain A: V.230, E.231 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Otake, K. et al., Optimization Efforts for Identification of Novel Highly Potent Keap1-Nrf2 Protein-Protein Interaction Inhibitors. J.Med.Chem. (2024)

Release Date

2024-05-22

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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