SMTL ID : 9hwq.1

Crystal structure of the Keap1 Kelch domain in complex with the XChem fragment Z19735904 at 1.14 Angstrom resolution.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.14 Å

Oligo State

monomer

Ligands

1 x B0A: ~{N}-cyclohexyl-2-phenoxy-ethanamide(Non-covalent)

B0A.1: 14 residues within 4Å: Chain A: Y.14, S.43, G.44, R.95, G.142, G.189, S.235, A.236, Y.252, F.257, S.282, G.283 Ligands: SO4.4, DMS.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.14, A:R.95, A:Y.252, A:F.257, A:F.257 Hydrogen bonds: A:G.44, A:S.282 Water bridges: A:S.43

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

SO4.2: 5 residues within 4Å: Chain A: I.115, H.116, H.117, S.118, S.119 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.118, A:S.118, A:S.118, A:S.119 Water bridges: A:S.119, A:S.119, A:R.139 Salt bridges: A:H.117 SO4.3: 4 residues within 4Å: Chain A: C.114, I.115, H.116, R.139 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.116 Water bridges: A:R.139, A:R.139, A:D.159 Salt bridges: A:H.116, A:R.139 SO4.4: 6 residues within 4Å: Chain A: S.43, R.60, N.62, N.94, R.95 Ligands: B0A.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.62, A:N.62, A:N.94 Water bridges: A:S.43 Salt bridges: A:R.95 SO4.5: 5 residues within 4Å: Chain A: H.104, E.124, P.125, E.126, R.127 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.126, A:R.127 Water bridges: A:R.127 Salt bridges: A:H.104, A:R.127 SO4.6: 8 residues within 4Å: Chain A: I.101, D.102, H.104, Y.106, R.122, R.150, P.172 Ligands: DMS.12 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.102, A:Y.106, A:Y.106 Water bridges: A:R.150 Salt bridges: A:H.104, A:R.122

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

DMS.7: 4 residues within 4Å: Chain A: R.34, L.35, A.36, D.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.37 Salt bridges: A:D.37 DMS.8: 3 residues within 4Å: Chain A: C.86, A.87, S.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.88 DMS.9: 6 residues within 4Å: Chain A: T.68, D.69, S.70, S.71, A.72, P.92 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.71, A:S.71, A:A.72 DMS.10: 7 residues within 4Å: Chain A: R.95, Y.205, Q.210, S.235, A.236, Y.252 Ligands: B0A.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.210, A:S.235 pi-Cation interactions: A:Y.205 DMS.11: 4 residues within 4Å: Chain A: S.118, L.137, T.138, R.139 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.139 DMS.12: 5 residues within 4Å: Chain A: H.104, R.122, E.124, R.127 Ligands: SO4.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.122, A:R.122, A:R.127, A:R.127 DMS.13: 3 residues within 4Å: Chain A: A.134, R.174, N.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.175 DMS.14: 5 residues within 4Å: Chain A: C.75, S.84, P.85, C.86, D.128 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.128 DMS.15: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, C. et al., Fragment-Based Drug Discovery of Novel High-affinity, Selective, and Anti-inflammatory Inhibitors of the Keap1-Nrf2 Protein-Protein Interaction. Angew.Chem.Int.Ed.Engl. (2025)

Release Date

2025-09-03

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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