SMTL ID : 6zf5.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.29 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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.118, 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 SO4.2: 2 residues within 4Å: Chain A: R.174, R.178 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.178, A:R.178 Salt bridges: A:R.174, A:R.178

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

DMS.3: 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.4: 4 residues within 4Å: Chain A: A.134, R.174, N.175, E.176 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: 7 residues within 4Å: Chain A: S.118, P.135, M.136, L.137, T.138, R.139 Ligands: DMS.13 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.139 DMS.7: 4 residues within 4Å: Chain A: H.104, R.122, E.124 Ligands: DMS.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.122, A:R.122 Salt bridges: A:E.124 DMS.8: 7 residues within 4Å: Chain A: R.163, Y.205, Q.210, S.235, A.236, Y.252 Ligands: QH8.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.210, A:S.235 pi-Cation interactions: A:Y.205 DMS.9: 2 residues within 4Å: Chain A: N.212, H.233 No protein-ligand interaction detected (PLIP) DMS.10: 2 residues within 4Å: Chain A: A.87, S.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.88 DMS.11: 4 residues within 4Å: Chain A: C.48, V.49, V.100, A.287 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.49 DMS.12: 4 residues within 4Å: Chain A: R.60, R.95, G.113, C.114 1 PLIP interactions: 1 interactions with chain A Water bridges: A:C.114 DMS.13: 2 residues within 4Å: Chain A: R.139 Ligands: DMS.6 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.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.16: 4 residues within 4Å: Chain A: Y.14, R.60, N.62 Ligands: QH8.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.60 DMS.17: 5 residues within 4Å: Chain A: R.6, V.241, H.242, Q.243, V.288 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.243 Water bridges: A:G.244

1 x QH8: 1-[3-[(4-butylphenyl)sulfonyl-(2-hydroxy-2-oxoethyl)amino]phenyl]-5-cyclopropyl-pyrazole-4-carboxylic acid(Non-covalent)

QH8.18: 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.8, DMS.16 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.14, A:Y.14, A:I.141, A:A.236, A:Y.252, A:Y.252, A:Y.252, A:F.257 Hydrogen bonds: A:N.94, A:S.188 Water bridges: A:R.60, A:R.60 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