MolNFT v1 · #169179 · protein
Crystal structure of PT3388 bound to HIF2A-B*:ARNT-B* complex
6X3D · Endothelial pas domain-containing protein 1: “Crystal structure of PT3388 bound to HIF2A-B*:ARNT-B* complex”. X-ray diffraction, 1 ligand (ULM), 2 pockets (best druggability 0.78). MolNFT v1 #169179 on GenesisL1: 3D structure…
- PDB
- 6X3D
- Type
- protein
- Length
- 211 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
- ULM
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endothelial pas domain-containing protein 1 | protein | 104 | 31% helix, 38% strand | Q99814 |
| B | Aryl hydrocarbon receptor nuclear translocator | protein | 107 | 22% helix, 37% strand | P27540 |
Ligands and binding sites
- ULM · (6R,7S)-4-[(3,3-difluorocyclobutyl)oxy]-6-fluoro-1-(trifluoromethyl)-6,7-dihydro-5H-cyclopenta[c]pyridin-7-ol · 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 | 100 | 0.78 | 0.98 | 26 | ULM |
| 2 | 144 | 0.50 | 0.79 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 504 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6X3D · Crystal structure of PT3388 bound to HIF2a-B*:ARNT-B* complex · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.96
- 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
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 6X3D · PDBe 6X3D · UniProt Q99814 · UniProt P27540
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