SMTL ID : 6zf6.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

monomer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.174, R.178 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.178 Salt bridges: A:R.174, A:R.178 SO4.2: 2 residues within 4Å: Chain A: N.212, H.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.212 Salt bridges: A:H.233 SO4.3: 4 residues within 4Å: Chain A: A.36, D.37, N.81 Ligands: DMS.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.37 Water bridges: A:N.81 SO4.4: 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 SO4.5: 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.119, A:S.119 Water bridges: A:S.118, A:S.119, A:R.139 Salt bridges: A:H.117

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

DMS.6: 5 residues within 4Å: Chain A: A.134, R.174, N.175, E.176 Ligands: DMS.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.175 DMS.7: 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.8: 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.9: 4 residues within 4Å: Chain A: H.104, R.122, E.124 Ligands: DMS.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.122, A:R.122 DMS.10: 7 residues within 4Å: Chain A: R.163, Y.205, Q.210, S.235, A.236, Y.252 Ligands: QH2.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.210, A:S.235 pi-Cation interactions: A:Y.205 DMS.11: 2 residues within 4Å: Chain A: A.87, S.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.88 DMS.12: 8 residues within 4Å: Chain A: G.47, C.48, V.49, V.100, T.240, V.286, A.287, V.288 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.49 DMS.13: 1 residues within 4Å: Chain A: R.139 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.139 DMS.14: 7 residues within 4Å: Chain A: F.158, T.161, N.162, R.163, I.186, D.206, G.207 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.163 DMS.15: 8 residues within 4Å: Chain A: I.101, D.102, H.104, Y.106, R.122, R.150, P.172 Ligands: DMS.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.104, A:Y.106, A:R.122 DMS.16: 5 residues within 4Å: Chain A: R.34, L.35, A.36, D.37 Ligands: SO4.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.37 DMS.17: 8 residues within 4Å: Chain A: R.95, S.111, G.113, C.114, H.116, I.141, F.158 Ligands: QH2.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.116 DMS.18: 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

1 x QH2: 1-[3-[2-hydroxy-2-oxoethyl(phenylsulfonyl)amino]phenyl]-5-[(1~{S},2~{S})-2-phenylcyclopropyl]pyrazole-4-carboxylic acid(Non-covalent)

QH2.19: 21 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.10, DMS.17 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.14, A:F.158, A:F.158, A:Y.252, A:Y.252, A:F.257 Hydrogen bonds: A:N.94, A:S.188, A:S.188 Water bridges: A:S.43 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

Related Entries With Identical Sequence