SMTL ID : 6zf7.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

monomer

Ligands

3 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.118, A:S.119, A:S.119 Water bridges: A:S.118, A:R.139 Salt bridges: A:H.117 SO4.2: 3 residues within 4Å: Chain A: W.130, H.131, L.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.132 Salt bridges: A:H.131 SO4.3: 6 residues within 4Å: Chain A: C.114, I.115, H.116, R.139, G.160 Ligands: DMS.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.116, A:D.159 Water bridges: A:C.114 Salt bridges: A:H.116, A:R.139

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

DMS.4: 5 residues within 4Å: Chain A: A.134, R.174, N.175, E.176 Ligands: DMS.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.175 DMS.5: 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.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 Hydrogen bonds: A:R.139 DMS.7: 4 residues within 4Å: Chain A: H.104, R.122, E.124 Ligands: DMS.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.122, A:R.122 DMS.8: 2 residues within 4Å: Chain A: A.87, S.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.88 DMS.9: 2 residues within 4Å: Chain A: R.139 Ligands: SO4.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.139 DMS.10: 8 residues within 4Å: Chain A: I.101, D.102, H.104, Y.106, R.122, R.150, P.172 Ligands: DMS.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.104, A:Y.106, A:R.122 Salt bridges: A:D.102 DMS.11: 1 residues within 4Å: Chain A: E.220 No protein-ligand interaction detected (PLIP) DMS.12: 4 residues within 4Å: Chain A: R.163, Y.205, G.207 Ligands: DMS.16 No protein-ligand interaction detected (PLIP) DMS.13: 5 residues within 4Å: Chain A: L.132, V.133, A.134, N.175 Ligands: DMS.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.175 DMS.14: 2 residues within 4Å: Chain A: N.212, H.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.212, A:H.233 DMS.15: 5 residues within 4Å: Chain A: N.162, R.163, I.186, D.206, G.207 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.163 DMS.16: 7 residues within 4Å: Chain A: R.163, Y.205, Q.210, S.235, Y.252 Ligands: DMS.12, QHQ.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.210, A:S.235 pi-Cation interactions: A:Y.205 DMS.17: 6 residues within 4Å: Chain A: R.6, V.241, H.242, Q.243, G.244, V.288 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.6, A:H.242, A:Q.243

1 x QHQ: 5-cyclopropyl-1-[3-[2-hydroxy-2-oxoethyl-(3-methoxyphenyl)sulfonyl-amino]phenyl]pyrazole-4-carboxylic acid(Non-covalent)

QHQ.18: 20 residues within 4Å: Chain A: Y.14, S.43, G.44, R.60, N.94, R.95, I.141, G.142, F.158, R.163, S.188, G.189, Y.205, S.235, A.236, Y.252, F.257, S.282, G.283 Ligands: DMS.16 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.14, A:R.95, A:Y.205, A:Y.252, A:Y.252 Hydrogen bonds: A:N.94, A:S.188, A:S.188 Salt bridges: A:R.60, A:R.95, A:R.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pallesen, J.S. et al., Deconstructing Noncovalent Kelch-like ECH-Associated Protein 1 (Keap1) Inhibitors into Fragments to Reconstruct New Potent Compounds. J.Med.Chem. (2021)

Release Date

2021-04-14

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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