Research workbench
Crystal structure of PT2440 bound to HIF2A-B*:ARNT-B* complex
Analyse Crystal structure of PT2440 bound to HIF2A-B*:ARNT-B* complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D09
- Type
- protein
- Length
- 217 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endothelial pas domain-containing protein 1; Aryl hydrocarbon receptor nuclear…
- UniProt
- Q99814, P27540
- Ligands
- FOJ
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endothelial pas domain-containing protein 1 | protein | 107 | 32% helix, 36% strand | Q99814 |
| B | Aryl hydrocarbon receptor nuclear translocator | protein | 110 | 25% helix, 36% strand | P27540 |
Ligands and binding sites
- FOJ · 3-{[(3R)-4-(difluoromethyl)-2,2-difluoro-3-hydroxy-1,1-dioxo-2,3-dihydro-1H-1-benzothiophen-5-yl]oxy}-5-fluorobenzonitrile · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.80 | 0.97 | 27 | FOJ |
| 2 | 136 | 0.49 | 0.79 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 548 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6D09 · Crystal structure of PT2440 bound to HIF2a-B*:ARNT-B* complex · the same entry in another collection · chain A against A, TM-score 1.00
- P27540 · AlphaFold monomer V2.0 prediction for aryl hydrocarbon receptor nuclear translocator… · a predicted model of the same protein · chain B against A, TM-score 0.95
- Q99814 · AlphaFold monomer V2.0 prediction for endothelial pas domain- containing protein 1… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q99814
- Every structure of UniProt P27540
- Elsewhere: RCSB PDB 6D09 · PDBe 6D09 · UniProt Q99814 · UniProt P27540
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