SMTL ID : 7ofb.1

Keap1 kelch domain bound to a small molecule fragment

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.116, A:S.118, A:S.119, A:S.119 Salt bridges: A:H.117

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

DMS.2: 6 residues within 4Å: Chain A: S.118, P.135, M.136, L.137, T.138, R.139 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.139, A:R.139 DMS.3: 10 residues within 4Å: Chain A: Y.14, S.43, G.44, N.62, R.95, A.236, S.282, G.283 Ligands: DMS.4, VCN.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.282 DMS.4: 7 residues within 4Å: Chain A: S.43, R.60, N.62, N.94, R.95, S.111 Ligands: DMS.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.94 DMS.5: 6 residues within 4Å: Chain A: L.132, V.133, A.134, P.135, N.175 Ligands: DMS.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.175 DMS.6: 4 residues within 4Å: Chain A: A.134, R.174, N.175 Ligands: DMS.5 No protein-ligand interaction detected (PLIP) DMS.7: 5 residues within 4Å: Chain A: R.34, L.35, A.36, D.37, N.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.37 Salt bridges: A:D.37

1 x VCN: ~{N},~{N}-diethyl-9-oxidanylidene-fluorene-4-carboxamide(Non-covalent)

VCN.8: 13 residues within 4Å: Chain A: Y.14, R.95, R.163, S.188, G.189, Y.205, Q.210, S.235, A.236, Y.252, F.257, S.282 Ligands: DMS.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.252, A:F.257, A:F.257 Hydrogen bonds: A:Q.210, A:S.235 pi-Stacking: A:Y.205, A:Y.252, A:Y.252

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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