Research workbench
Structure of the human histamine H1 receptor in complex with doxepin
Analyse Structure of the human histamine H1 receptor in complex with doxepin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RZE
- Type
- protein
- Length
- 428 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histamine H1 receptor, lysozyme chimera
- EC
- 3.2.1.17
- UniProt
- P35367, P00720
- Ligands
- 5EH, D7V, PO4
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 72% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histamine H1 receptor, lysozyme chimera (EC 3.2.1.17) | protein | 428 | 72% helix, 4% strand | P35367, P00720 |
Ligands and binding sites
- 5EH · (3E)-3-(dibenzo[b,e]oxepin-11(6H)-ylidene)-N,N-dimethylpropan-1-amine · ligand · chains A
- D7V · (3Z)-3-(dibenzo[b,e]oxepin-11(6H)-ylidene)-N,N-dimethylpropan-1-amine · ligand · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.78 | 0.88 | 42 | 5EH, D7V, PO4 |
| 2 | 162 | 0.47 | 0.76 | 27 | empty |
| 3 | 60 | 0.30 | 0.75 | 13 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3RZE · Structure of the human histamine H1 receptor in complex with doxepin · the same entry in another collection · chain A against A, TM-score 1.00
- P35367 · AlphaFold monomer V2.0 prediction for histamine H1 receptor (P35367) · a predicted model of the same protein · chain A against A, TM-score 0.65
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 P35367
- Every structure of UniProt P00720
- Elsewhere: RCSB PDB 3RZE · PDBe 3RZE · UniProt P35367 · UniProt P00720
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