MolNFT v1 · #154154 · protein
Human endothelin receptor type-B in complex with inverse agonist IRL2500
6K1Q · Endothelin B RECEPTOR,ENDOLYSIN,ENDOTHELIN B receptor: “Human endothelin receptor type-B in complex with inverse agonist IRL2500”. X-ray diffraction, 2 ligands (D2U, PO4), 8 pockets (best druggability 0.75). MolNFT v1 #154154 on…
- PDB
- 6K1Q
- Type
- protein
- Length
- 410 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
- D2U, PO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 82% 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 | 410 | 82% helix, 4% strand | P24530, P00720 |
Ligands and binding sites
- D2U · (2~{S})-2-[[(2~{R})-2-[(3,5-dimethylphenyl)carbonyl-methyl-amino]-3-(4-phenylphenyl)propanoyl]amino]-3-(1~{H}-indol-3-yl)propanoic acid · ligand · chains A
- PO4 · Phosphate ion · ion · 4 copies · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.75 | 0.81 | 57 | D2U |
| 2 | 72 | 0.45 | 0.82 | 15 | empty |
| 3 | 144 | 0.45 | 0.76 | 22 | empty |
| 4 | 110 | 0.38 | 0.75 | 17 | empty |
| 5 | 82 | 0.36 | 0.76 | 20 | PO4 |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6K1Q · Human endothelin receptor type-B in complex with inverse agonist IRL2500 · 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 6K1Q · PDBe 6K1Q · UniProt P24530 · UniProt P00720
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