SMTL ID : 7ofe.1

Keap1 kelch domain bound to a small molecule inhibitor of the Keap1-Nrf2 protein-protein interaction

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.19 Å

Oligo State

monomer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: I.113, H.114, H.115, S.116, S.117 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.116, A:S.116, A:S.116, A:S.117, A:S.117 Water bridges: A:R.137 Salt bridges: A:H.115 SO4.2: 6 residues within 4Å: Chain A: C.112, I.113, H.114, R.137, D.157, G.158 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.114 Salt bridges: A:H.114, A:R.137

7 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 5 residues within 4Å: Chain A: R.58, N.60, N.92, R.93 Ligands: DMS.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.60, A:N.92 DMS.4: 3 residues within 4Å: Chain A: W.128, H.129, L.130 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.130 DMS.5: 10 residues within 4Å: Chain A: Y.12, S.41, G.42, N.60, R.93, A.234, S.280, G.281 Ligands: DMS.3, VBQ.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.280 DMS.6: 3 residues within 4Å: Chain A: A.132, R.172, N.173 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.173 DMS.7: 6 residues within 4Å: Chain A: S.116, P.133, M.134, L.135, T.136, R.137 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.137 DMS.8: 6 residues within 4Å: Chain A: T.66, D.67, S.68, S.69, A.70, P.90 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.69, A:S.69, A:A.70 Water bridges: A:S.68 DMS.9: 3 residues within 4Å: Chain A: H.102, R.120, E.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.120, A:R.120

1 x VBQ: 2-[(9-oxidanylidenefluoren-4-yl)carbonylamino]ethanoic acid(Non-covalent)

VBQ.10: 13 residues within 4Å: Chain A: Y.12, R.93, R.161, S.186, G.187, Y.203, Q.208, S.233, A.234, Y.250, F.255, S.280 Ligands: DMS.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.234, A:Y.250, A:F.255, A:F.255 Hydrogen bonds: A:R.161, A:S.186, A:S.186, A:Q.208, A:S.233 Salt bridges: A:R.93 pi-Stacking: A:Y.203, A:Y.250, A:Y.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Narayanan, D. et al., Development of Noncovalent Small-Molecule Keap1-Nrf2 Inhibitors by Fragment-Based Drug Discovery. J.Med.Chem. (2022)

Release Date

2022-11-02

Peptides

Kelch-like ECH-associated protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Kelch-like ECH-associated protein 1