SMTL ID : 4l7d.1

Structure of keap1 kelch domain with (1S,2R)-2-{[(1S)-5-methyl-1-[(1-oxo-1,3-dihydro-2H-isoindol-2-yl)methyl]-3,4-dihydroisoquinolin-2(1H)-yl]carbonyl}cyclohexanecarboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-trimer

Ligands

3 x 1VX: (1S,2R)-2-{[(1S)-5-methyl-1-[(1-oxo-1,3-dihydro-2H-isoindol-2-yl)methyl]-3,4-dihydroisoquinolin-2(1H)-yl]carbonyl}cyclohexanecarboxylic acid(Non-covalent)

1VX.1: 11 residues within 4Å: Chain A: Y.17, N.97, R.98, G.145, G.192, A.239, Y.255, F.260, S.285, G.286 Ligands: ACT.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.17, A:Y.17, A:R.98, A:A.239, A:F.260 Hydrogen bonds: A:N.97, A:S.285 Water bridges: A:R.98, A:R.98 Salt bridges: A:R.63, A:R.98 pi-Stacking: A:Y.255, A:Y.255 1VX.4: 14 residues within 4Å: Chain B: Y.17, R.63, N.65, N.97, R.98, G.145, G.192, A.239, Y.255, F.260, S.285, G.286 Ligands: ACT.5, ACT.6 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.17, B:Y.17, B:Y.17, B:A.239, B:F.260 Hydrogen bonds: B:N.97, B:S.285 Salt bridges: B:R.63, B:R.98 pi-Stacking: B:Y.255, B:Y.255 1VX.8: 14 residues within 4Å: Chain C: Y.17, S.46, G.47, R.63, N.65, N.97, R.98, G.192, A.239, Y.255, F.260, S.285, G.286 Ligands: ACT.10 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:Y.17, C:Y.17, C:Y.17, C:R.98, C:A.239, C:F.260 Hydrogen bonds: C:N.97, C:S.285 Water bridges: C:R.98 Salt bridges: C:R.63, C:R.98 pi-Stacking: C:Y.255

10 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 4 residues within 4Å: Chain A: Y.208, Q.213, S.238 Ligands: 1VX.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.208 Hydrogen bonds: A:Q.213, A:S.238 ACT.3: 5 residues within 4Å: Chain A: L.154, Y.174, P.175, E.176, R.177 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.154 Hydrogen bonds: A:E.176, A:R.177 Salt bridges: A:R.177 ACT.5: 6 residues within 4Å: Chain B: R.98, F.161, R.166, S.191 Ligands: 1VX.4, ACT.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.191 Water bridges: B:R.98 Salt bridges: B:R.98, B:R.166 ACT.6: 6 residues within 4Å: Chain B: Y.208, Q.213, S.238, Y.255 Ligands: 1VX.4, ACT.5 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.208 Hydrogen bonds: B:Q.213, B:S.238 ACT.7: 4 residues within 4Å: Chain B: D.209 Chain C: D.162, T.164, N.165 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.164, C:N.165 ACT.9: 4 residues within 4Å: Chain C: R.98, F.161, R.166, S.191 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.161 Hydrogen bonds: C:S.191, C:S.191 Water bridges: C:R.98 Salt bridges: C:R.98, C:R.166 ACT.10: 5 residues within 4Å: Chain C: Y.208, Q.213, S.238, Y.255 Ligands: 1VX.8 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.208 Hydrogen bonds: C:Q.213, C:Q.213, C:S.238 ACT.11: 5 residues within 4Å: Chain C: L.154, Y.174, P.175, E.176, R.177 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.154 Hydrogen bonds: C:E.176, C:R.177 Water bridges: C:R.153 Salt bridges: C:R.177 ACT.12: 7 residues within 4Å: Chain C: Y.12, V.52, G.55, L.56, L.57, P.81, T.292 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.12, C:P.81 Hydrogen bonds: C:Y.12, C:Y.12 ACT.13: 5 residues within 4Å: Chain A: G.163, T.164 Chain C: C.117, I.118, H.119 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.119 Salt bridges: C:H.119, C:R.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jnoff, E. et al., Binding Mode and Structure-Activity Relationships around Direct Inhibitors of the Nrf2-Keap1 Complex. Chemmedchem (2014)

Release Date

2014-02-19

Peptides

Kelch-like ECH-associated protein 1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Kelch-like ECH-associated protein 1

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