SMTL ID : 8ivg.1

Methyl and Fluorine Effects in Novel Orally Bioavailable Keap1/Nrf2 PPI Inhibitor for Treatment of Chronic Kidney Disease

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x SGO: (3S)-3-(4-methylphenyl)-3-[2-(5,6,7,8-tetrahydronaphthalen-2-yl)ethanoylamino]propanoic acid(Non-covalent)

SGO.1: 17 residues within 4Å: Chain A: Y.25, G.55, 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 Ligands: DTT.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.25, A:R.106, A:I.152, A:Y.216, A:A.247, A:Y.263, A:Y.263, A:Y.263, A:F.268, A:F.268 Hydrogen bonds: A:S.199, A:S.199, A:S.246 Water bridges: A:R.106, A:R.106 Salt bridges: A:R.106, A:R.174

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.2: 9 residues within 4Å: Chain A: Y.25, S.54, R.71, N.73, N.105, R.106, S.293, G.294 Ligands: SGO.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.106, A:R.106

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

SO4.3: 5 residues within 4Å: Chain A: H.115, E.135, P.136, E.137, R.138 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.137, A:R.138 Water bridges: A:R.138 Salt bridges: A:H.115, A:R.138 SO4.4: 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 Hydrogen bonds: A:I.112 Water bridges: A:R.161, A:R.161 Salt bridges: A:H.115, A:R.133 SO4.5: 4 residues within 4Å: Chain A: H.115, R.133, E.135, R.138 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.115 Water bridges: A:R.138 Salt bridges: A:R.133, A:R.138 SO4.6: 4 residues within 4Å: Chain A: I.126, H.128, N.129, S.130 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.129, A:N.129, A:S.130, A:S.130 Water bridges: A:N.129, A:N.129, A:N.129 Salt bridges: A:H.128 SO4.7: 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 SO4.8: 3 residues within 4Å: Chain A: W.141, H.142, L.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.143 Salt bridges: A:H.142 SO4.9: 2 residues within 4Å: Chain A: P.52, N.72 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.72 Water bridges: A:S.31 SO4.10: 6 residues within 4Å: Chain A: A.12, R.17, V.252, H.253, Q.254, V.299 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.254 Water bridges: A:G.255 Salt bridges: A:R.17, A:H.253 SO4.11: 2 residues within 4Å: Chain A: R.71, G.124 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.124 Water bridges: A:R.71, A:R.71 Salt bridges: A:R.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Otake, K. et al., Methyl and Fluorine Effects in Novel Orally Bioavailable Keap1-Nrf2 PPI Inhibitor. Acs Med.Chem.Lett. (2023)

Release Date

2023-06-14

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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