MolNFT v1 · #168452 · protein
Crystal structure of HTR2A with inverse agonist
6WH4 · 5-hydroxytryptamine receptor 2A,SOLUBLE cytochrome B562…: “Crystal structure of HTR2A with inverse agonist”. X-ray diffraction, 4 ligands (OLA, 89F, CLR), 15 pockets (best druggability 0.82). MolNFT v1 #168452 on GenesisL1: 3D…
- PDB
- 6WH4
- Type
- protein
- Length
- 1,111 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-hydroxytryptamine receptor 2A,SOLUBLE cytochrome B562 fusion
- UniProt
- P28223, P0ABE7
- Ligands
- OLA, 89F, CLR, NDS
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 80% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-hydroxytryptamine receptor 2A,SOLUBLE cytochrome B562 fusion | protein | 378 | 79% helix, 1% strand | P28223, P0ABE7 |
| B | 5-hydroxytryptamine receptor 2A,SOLUBLE cytochrome B562 fusion | protein | 358 | 81% helix, 1% strand | P28223, P0ABE7 |
| C | 5-hydroxytryptamine receptor 2A,SOLUBLE cytochrome B562 fusion | protein | 375 | 81% helix, 1% strand | P28223, P0ABE7 |
Ligands and binding sites
- OLA · Oleic acid · ligand · 4 copies · chains A, B, C
- 89F · 1-methyl-4-[(5~{S})-3-methylsulfanyl-5,6-dihydrobenzo[b][1]benzothiepin-5-yl]piperazine · ligand · 3 copies · chains A, B, C
- CLR · Cholesterol · ligand · 2 copies · chains A, C
- NDS · Ethyl dimethyl ammonio propane sulfonate · ligand · chains C
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C
- 1PE · Pentaethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 637 | 0.82 | 0.86 | 66 | 89F, 1PE |
| 2 | 568 | 0.82 | 0.87 | 51 | 89F, PEG |
| 3 | 610 | 0.80 | 0.85 | 55 | 89F, PEG |
| 4 | 403 | 0.72 | 0.83 | 57 | empty |
| 5 | 462 | 0.63 | 0.77 | 56 | empty |
Interfaces
2 interfaces between chains.
- B–C · 465 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 197 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6WH4 · Crystal structure of HTR2A with inverse agonist · the same entry in another collection · chain A against A, TM-score 1.00
- P28223 · AlphaFold monomer V2.0 prediction for 5-hydroxytryptamine receptor 2A (P28223) · a predicted model of the same protein · chain B against A, TM-score 0.84
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A against A, TM-score 0.27
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 P28223
- Every structure of UniProt P0ABE7
- Elsewhere: RCSB PDB 6WH4 · PDBe 6WH4 · UniProt P28223 · UniProt P0ABE7
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