Research workbench
Structure of the human smoothened 7TM receptor in complex with an antitumor agent
Analyse Structure of the human smoothened 7TM receptor in complex with an antitumor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JKV
- Type
- protein
- Length
- 904 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562, smoothened homolog
- UniProt
- P0ABE7, Q99835
- Ligands
- OLA, 1KS
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble cytochrome B562, smoothened homolog | protein | 454 | 70% helix, 5% strand | P0ABE7, Q99835 |
| B | Soluble cytochrome B562, smoothened homolog | protein | 450 | 72% helix, 4% strand | P0ABE7, Q99835 |
Ligands and binding sites
- OLA · Oleic acid · ligand · 3 copies · chains A, B
- 1KS · 4-fluoro-N-methyl-N-{1-[4-(1-methyl-1H-pyrazol-5-yl)phthalazin-1-yl]piperidin-4-yl}-2-(trifluoromethyl)benzamide · ligand · 2 copies · chains A, B
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 5 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.85 | 0.95 | 56 | 1KS |
| 2 | 448 | 0.82 | 0.89 | 75 | 1KS |
| 3 | 469 | 0.77 | 0.85 | 64 | empty |
| 4 | 342 | 0.63 | 0.79 | 40 | empty |
| 5 | 438 | 0.59 | 0.75 | 46 | empty |
Interfaces
1 interface between chains.
- A–B · 1218 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4JKV · Structure of the human smoothened 7TM receptor in complex with an antitumor agent · the same entry in another collection · chain A against A, TM-score 1.00
- Q99835 · AlphaFold monomer V2.0 prediction for smoothened homolog (Q99835) · a predicted model of the same protein · chain B against A, TM-score 0.76
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain B against A, TM-score 0.23
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 P0ABE7
- Every structure of UniProt Q99835
- Elsewhere: RCSB PDB 4JKV · PDBe 4JKV · UniProt P0ABE7 · UniProt Q99835
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