SMTL ID : 6v6z.4 (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

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

FMT.1: 6 residues within 4Å: Chain A: I.102, D.103, H.105, Y.107, R.123, R.151 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.105, A:R.123, A:R.151 FMT.2: 2 residues within 4Å: Chain A: G.255, H.256 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.256 Water bridges: A:Y.253 FMT.3: 4 residues within 4Å: Chain A: Y.172, P.173, E.174, R.175 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.174, A:R.175, A:R.175 Water bridges: A:R.151 FMT.5: 4 residues within 4Å: Chain A: V.193, I.240, V.287 Ligands: NA.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.193 Water bridges: A:G.48, A:I.240, A:T.241, A:V.287 FMT.6: 4 residues within 4Å: Chain A: C.115, I.116, H.117, R.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.117 FMT.7: 3 residues within 4Å: Chain A: S.120, L.133, P.136 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.120 FMT.11: 3 residues within 4Å: Chain A: V.195, H.197, N.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.198 Water bridges: A:H.197, A:H.197 FMT.12: 2 residues within 4Å: Chain A: F.16, R.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.17, A:R.17 FMT.13: 4 residues within 4Å: Chain A: V.92, H.113, I.116, H.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.113, A:H.118 FMT.14: 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:Q.244, A:Q.244 Water bridges: A:G.245 FMT.15: 3 residues within 4Å: Chain A: I.102, D.103, R.151 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.103 Water bridges: A:G.104, A:R.151 FMT.16: 4 residues within 4Å: Chain A: Y.154, Y.172, I.181, Y.218 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.154, A:Y.172, A:Y.218 FMT.17: 6 residues within 4Å: Chain A: G.143, V.144, G.190, A.191 Ligands: Q5Y.4, FMT.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.190 Water bridges: A:A.191, A:A.191 FMT.18: 5 residues within 4Å: Chain A: L.46, A.47, V.285, G.286 Ligands: FMT.17 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.240 FMT.19: 4 residues within 4Å: Chain A: V.146, A.147, V.148, V.195 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.148 Water bridges: A:V.99, A:V.146, A:V.195

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

Q5Y.4: 17 residues within 4Å: Chain A: Y.15, S.44, G.45, N.63, N.95, R.96, S.189, G.190, Y.206, Q.211, S.236, A.237, Y.253, F.258, S.283, G.284 Ligands: FMT.17 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.15, A:Y.15, A:R.96, A:Y.206, A:A.237, A:Y.253, A:Y.253 Hydrogen bonds: A:S.44, A:N.63, A:N.95, A:R.96, A:Q.211, A:A.237 Water bridges: A:S.189, A:S.189, A:S.189, A:S.189 Salt bridges: A:R.96 pi-Stacking: A:F.258 pi-Cation interactions: A:R.96

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

NA.8: 3 residues within 4Å: Chain A: V.146, V.193 Ligands: FMT.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.146, A:V.146 NA.10: 1 residues within 4Å: Chain A: W.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.131 Water bridges: A:W.131

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.9: 6 residues within 4Å: Chain A: Y.15, R.17, N.63, S.64, P.65, N.68 No protein-ligand interaction detected (PLIP)

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
D

Kelch-like ECH-associated protein 1

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