SMTL ID : 6zf8.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.118, A:S.118, A:S.119, A:S.119 Water bridges: A:R.139 Salt bridges: A:H.117 SO4.2: 7 residues within 4Å: Chain A: C.114, I.115, H.116, R.139, D.159, G.160 Ligands: DMS.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.116 Salt bridges: A:H.116, A:R.139

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

DMS.3: 4 residues within 4Å: Chain A: A.134, R.174, N.175 Ligands: DMS.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.175 DMS.4: 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.5: 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.6: 5 residues within 4Å: Chain A: H.104, R.122, E.124, R.127 Ligands: DMS.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.122, A:R.122, A:R.127 Salt bridges: A:E.124 DMS.7: 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.8: 2 residues within 4Å: Chain A: R.139 Ligands: SO4.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.139 DMS.9: 8 residues within 4Å: Chain A: I.101, D.102, H.104, Y.106, R.122, R.150, P.172 Ligands: DMS.6 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.10: 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 DMS.11: 5 residues within 4Å: Chain A: L.132, V.133, A.134, N.175 Ligands: DMS.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.175 DMS.12: 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.13: 6 residues within 4Å: Chain A: R.163, Y.205, Q.210, S.235, Y.252 Ligands: QHZ.17 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.205 DMS.14: 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.15: 4 residues within 4Å: Chain A: R.231, H.232, E.273, R.276 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.232 Salt bridges: A:E.273 DMS.16: 4 residues within 4Å: Chain A: R.60, N.67, R.95, G.113 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.60, A:R.60

1 x QHZ: 1-[3-[2-hydroxy-2-oxoethyl-(3-methoxyphenyl)sulfonyl-amino]phenyl]-5-[(1~{S},2~{S})-2-phenylcyclopropyl]pyrazole-4-carboxylic acid(Non-covalent)

QHZ.17: 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.13 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.14, A:R.95, A:I.141, A:F.158, A:F.158, A:A.236, A:Y.252, A:Y.252, A:F.257 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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