Research workbench
Crystal structure of the heterodimeric hif-2 complex with antagonist PT2385
Analyse Crystal structure of the heterodimeric hif-2 complex with antagonist PT2385 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E3S
- Type
- protein
- Length
- 540 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aryl hydrocarbon receptor nuclear translocator; Endothelial pas domain-containing protein…
- UniProt
- P53762, P97481
- Ligands
- 79A
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aryl hydrocarbon receptor nuclear translocator | protein | 250 | 38% helix, 34% strand | P53762 |
| B | Endothelial pas domain-containing protein 1 | protein | 290 | 36% helix, 30% strand | P97481 |
Ligands and binding sites
- 79A · 3-{[(1S)-2,2-difluoro-1-hydroxy-7-(methylsulfonyl)-2,3-dihydro-1H-inden-4-yl]oxy}-5-fluorobenzonitrile · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.81 | 0.97 | 30 | 79A |
| 2 | 272 | 0.67 | 0.83 | 47 | empty |
| 3 | 151 | 0.62 | 0.84 | 29 | empty |
| 4 | 355 | 0.60 | 0.77 | 33 | empty |
| 5 | 67 | 0.29 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3496 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6E3S · Crystal Structure of the Heterodimeric HIF-2 Complex with Antagonist PT2385 · the same entry in another collection · chain A against A, TM-score 1.00
- P97481 · AlphaFold monomer V2.0 prediction for endothelial pas domain- containing protein 1… · a predicted model of the same protein · chain B against A, TM-score 0.97
- P53762 · AlphaFold monomer V2.0 prediction for aryl hydrocarbon receptor nuclear translocator… · a predicted model of the same protein · chain A against A, TM-score 0.87
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 P53762
- Every structure of UniProt P97481
- Elsewhere: RCSB PDB 6E3S · PDBe 6E3S · UniProt P53762 · UniProt P97481
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