SMTL ID : 7ofd.1

Keap1 kelch domain bound to a small molecule fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: I.115, H.116, H.117, S.118, S.119 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.118, A:S.118, A:S.118, A:S.119, A:S.119 Water bridges: A:R.139 Salt bridges: A:H.117 SO4.2: 6 residues within 4Å: Chain A: C.114, I.115, H.116, R.139, D.159, G.160 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.116 Salt bridges: A:H.116, A:R.139

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

DMS.3: 5 residues within 4Å: Chain A: R.60, N.62, N.94, R.95 Ligands: VBW.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.62, A:N.94 DMS.4: 3 residues within 4Å: Chain A: W.130, H.131, L.132 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.132 DMS.5: 4 residues within 4Å: Chain A: A.134, R.174, N.175 Ligands: DMS.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.175 DMS.6: 5 residues within 4Å: Chain A: S.118, M.136, L.137, T.138, R.139 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.139 DMS.7: 6 residues within 4Å: Chain A: T.68, D.69, S.70, S.71, A.72, P.92 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.70, A:S.71, A:S.71, A:A.72 DMS.8: 3 residues within 4Å: Chain A: H.104, R.122, E.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.122, A:R.122 DMS.9: 2 residues within 4Å: Chain A: N.212, H.233 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.233 DMS.10: 4 residues within 4Å: Chain A: R.34, L.35, A.36, D.37 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.37 DMS.11: 5 residues within 4Å: Chain A: Y.205, Q.210, S.235, Y.252 Ligands: VBW.14 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.205 DMS.12: 6 residues within 4Å: Chain A: L.132, V.133, A.134, P.135, N.175 Ligands: DMS.5 No protein-ligand interaction detected (PLIP) DMS.13: 2 residues within 4Å: Chain A: V.219, E.220 No protein-ligand interaction detected (PLIP)

1 x VBW: 6-fluoranyl-2-methyl-quinolin-4-ol(Non-covalent)

VBW.14: 9 residues within 4Å: Chain A: Y.14, S.43, N.62, A.236, Y.252, F.257, S.282 Ligands: DMS.3, DMS.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.252 Hydrogen bonds: A:S.282 pi-Stacking: A:Y.14, A:F.257

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

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