SMTL ID : 6v6z.1 (3 other biounits)

Crystal structure of N-[(4-methoxyphenyl)sulfonyl]-N-(4-{[(4-methoxyphenyl)sulfonyl]amino}naphthalen-1-yl)glycine bound to human Keap1 Kelch domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

11 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 4 residues within 4Å: Chain A: Y.172, P.173, E.174, R.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.174, A:R.175, A:R.175 FMT.2: 3 residues within 4Å: Chain A: R.7, H.243, Q.244 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.7, A:H.243, A:Q.244 Water bridges: A:G.245 FMT.4: 5 residues within 4Å: Chain A: V.92, H.113, I.116, H.118 Ligands: FMT.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.113 FMT.6: 4 residues within 4Å: Chain A: C.194, V.195, T.241, V.242 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.195, A:V.195, A:T.241, A:V.242 FMT.7: 3 residues within 4Å: Chain A: H.118, S.120 Ligands: FMT.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.118, A:S.120 FMT.10: 2 residues within 4Å: Chain A: R.96 Ligands: Q5Y.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.96 FMT.11: 7 residues within 4Å: Chain A: R.96, I.142, G.143, F.159, R.164, S.189 Ligands: Q5Y.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.96, A:I.142, A:R.164, A:R.164 FMT.12: 1 residues within 4Å: Chain A: N.185 No protein-ligand interaction detected (PLIP) FMT.13: 1 residues within 4Å: Chain A: R.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.175 Water bridges: A:E.177 FMT.14: 3 residues within 4Å: Chain A: Y.172, R.175, E.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.177 FMT.15: 5 residues within 4Å: Chain A: L.149, N.150, L.152, Y.154, V.220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.150

1 x Q5Y: N-[(4-methoxyphenyl)sulfonyl]-N-(4-{[(4-methoxyphenyl)sulfonyl]amino}naphthalen-1-yl)glycine(Non-covalent)

Q5Y.3: 18 residues within 4Å: Chain A: Y.15, S.44, G.45, N.63, N.95, R.96, R.164, S.189, G.190, Y.206, S.236, A.237, Y.253, F.258, S.283, G.284 Ligands: FMT.10, FMT.11 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.15, A:Y.15, A:R.96, A:Y.206, A:A.237 Hydrogen bonds: A:S.44, A:N.63, A:N.63, A:N.95, A:R.96 Water bridges: A:R.96, A:R.96 Salt bridges: A:R.61, A:R.96 pi-Stacking: A:Y.206 pi-Cation interactions: A:R.96

3 x NA: SODIUM ION(Non-functional Binders)

NA.5: 0 residues within 4Å: (No contacts) 4 PLIP interactions: 4 interactions with chain A Water bridges: A:G.48, A:V.99, A:V.146, A:V.193 NA.8: 1 residues within 4Å: Chain A: W.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.131, A:W.131 NA.9: 1 residues within 4Å: Chain A: T.279 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.277

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lazzara, P.R. et al., Synthesis and Evaluation of Noncovalent Naphthalene-Based KEAP1-NRF2 Inhibitors. Acs Med.Chem.Lett. (2020)

Release Date

2020-04-29

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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