SMTL ID : 6zf4.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.21 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 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: 3 residues within 4Å: Chain A: R.60, N.67, G.113 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.67 Water bridges: A:R.95, A:R.95, A:R.95, A:R.95 Salt bridges: A:R.60 SO4.3: 5 residues within 4Å: Chain A: C.114, I.115, H.116, R.139, G.160 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

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

DMS.4: 8 residues within 4Å: Chain A: I.101, D.102, H.104, Y.106, R.122, R.150, P.172 Ligands: DMS.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.104, A:Y.106, A:R.122 DMS.5: 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.6: 3 residues within 4Å: Chain A: C.86, A.87, S.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.88, A:S.88 DMS.7: 3 residues within 4Å: Chain A: A.134, R.174, N.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.175 DMS.8: 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.9: 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.10: 4 residues within 4Å: Chain A: R.231, H.232, E.273, R.276 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.273 DMS.11: 5 residues within 4Å: Chain A: R.163, Y.205, G.207 Ligands: DMS.14, DMS.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.163, A:R.163 DMS.12: 5 residues within 4Å: Chain A: S.118, M.136, L.137, T.138, R.139 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.139 DMS.13: 4 residues within 4Å: Chain A: H.104, R.122, R.127 Ligands: DMS.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.122, A:R.122 Salt bridges: A:E.124 DMS.14: 7 residues within 4Å: Chain A: R.163, Y.205, Q.210, S.235, Y.252 Ligands: DMS.11, QHW.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.210, A:S.235 pi-Cation interactions: A:Y.205 DMS.15: 6 residues within 4Å: Chain A: R.95, I.141, F.158, R.163 Ligands: DMS.11, QHW.19 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.95 DMS.16: 5 residues within 4Å: Chain A: R.6, 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.17: 5 residues within 4Å: Chain A: N.162, R.163, I.186, D.206, G.207 No protein-ligand interaction detected (PLIP) DMS.18: 10 residues within 4Å: Chain A: G.47, C.48, V.49, V.98, G.99, V.100, T.240, V.286, A.287, V.288 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.49

1 x QHW: 5-cyclopropyl-1-[3-[2-hydroxy-2-oxoethyl-(2,3,5,6-tetramethylphenyl)sulfonyl-amino]phenyl]pyrazole-4-carboxylic acid(Non-covalent)

QHW.19: 22 residues within 4Å: Chain A: Y.14, S.43, G.44, R.60, N.62, 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.14, DMS.15 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.14, A:Y.14, A:Y.14, A:R.95, A:Y.205, A:A.236, A:Y.252 Hydrogen bonds: A:N.94, A:S.188, A:S.282 Water bridges: A:S.43, A:R.95 Salt bridges: 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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