Research workbench
Human endothelin receptor type-B in complex with antagonist K-8794
Analyse Human endothelin receptor type-B in complex with antagonist K-8794 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X93
- Type
- protein
- Length
- 430 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endothelin B RECEPTOR,ENDOLYSIN,ENDOTHELIN B receptor
- EC
- 3.2.1.17
- UniProt
- P24530, P00720
- Ligands
- K87, CLR, SO4
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endothelin B RECEPTOR,ENDOLYSIN,ENDOTHELIN B receptor (EC 3.2.1.17) | protein | 430 | 79% helix, 4% strand | P24530, P00720 |
Ligands and binding sites
- K87 · 3-[6-[(4-tert-butylphenyl)sulfonylamino]-5-(2-methoxyphenoxy)-2-pyrimidin-2-yl-pyrimidin-4-yl]oxy-N-(2,6-dimethylphenyl)propanamide · ligand · chains A
- CLR · Cholesterol · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 11 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.77 | 0.79 | 73 | K87 |
| 2 | 238 | 0.57 | 0.78 | 28 | SO4 |
| 3 | 118 | 0.42 | 0.76 | 16 | empty |
| 4 | 85 | 0.35 | 0.75 | 13 | empty |
| 5 | 59 | 0.33 | 0.76 | 15 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5X93 · Human endothelin receptor type-B in complex with antagonist K-8794 · the same entry in another collection · chain A against A, TM-score 1.00
- P24530 · AlphaFold monomer V2.0 prediction for endothelin receptor type B (P24530) · a predicted model of the same protein · chain A against A, TM-score 0.69
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 P24530
- Every structure of UniProt P00720
- Elsewhere: RCSB PDB 5X93 · PDBe 5X93 · UniProt P24530 · UniProt P00720
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