Research workbench
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
Analyse Structure of KEAP1 kelch domain with (1S,2R)-2-{[(1S)-5-methyl-1-[(1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L7D
- Type
- protein
- Length
- 858 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kelch-like ech-associated protein 1
- UniProt
- Q14145
- Ligands
- 1VX
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kelch-like ech-associated protein 1 | protein | 286 | 0% helix, 52% strand | Q14145 |
| B | Kelch-like ech-associated protein 1 | protein | 285 | 0% helix, 51% strand | Q14145 |
| C | Kelch-like ech-associated protein 1 | protein | 287 | 0% helix, 53% strand | Q14145 |
Ligands and binding sites
- 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 · ligand · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · 10 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.79 | 0.81 | 94 | 1VX, ACT |
| 2 | 676 | 0.77 | 0.82 | 60 | 1VX, ACT |
| 3 | 663 | 0.76 | 0.81 | 56 | 1VX, ACT |
| 4 | 155 | 0.54 | 0.80 | 21 | empty |
| 5 | 83 | 0.36 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 717 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 272 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 146 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4L7D · Structure of keap1 kelch domain with (1S,2R)-2-{[(1S)-5-methyl-1-[(1-oxo-1,3-dihydro-2H-is… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q14145
- Elsewhere: RCSB PDB 4L7D · PDBe 4L7D · UniProt Q14145
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