Research workbench
Structure of human smoothened in complex with vismodegib
Analyse Structure of human smoothened in complex with vismodegib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L7I
- Type
- protein
- Length
- 1,136 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Smoothened HOMOLOG,SOLUBLE cytochrome B562,SMOOTHENED homolog
- UniProt
- Q99835, P0ABE7
- Ligands
- VIS, MPG, NAG, NA
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Smoothened HOMOLOG,SOLUBLE cytochrome B562,SMOOTHENED homolog | protein | 564 | 66% helix, 6% strand | Q99835, P0ABE7 |
| B | Smoothened HOMOLOG,SOLUBLE cytochrome B562,SMOOTHENED homolog | protein | 572 | 64% helix, 7% strand | Q99835, P0ABE7 |
Ligands and binding sites
- VIS · 2-chloranyl-~{N}-(4-chloranyl-3-pyridin-2-yl-phenyl)-4-methylsulfonyl-benzamide · ligand · 2 copies · chains A, B
- MPG · [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- NA · Sodium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.82 | 0.90 | 44 | VIS |
| 2 | 405 | 0.79 | 0.88 | 48 | VIS |
| 3 | 92 | 0.78 | 0.98 | 29 | empty |
| 4 | 93 | 0.77 | 0.98 | 24 | empty |
| 5 | 886 | 0.68 | 0.73 | 69 | MPG |
Interfaces
1 interface between chains.
- A–B · 472 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5L7I · Structure of human Smoothened in complex with Vismodegib · 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 0.82
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A against A, TM-score 0.18
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 Q99835
- Every structure of UniProt P0ABE7
- Elsewhere: RCSB PDB 5L7I · PDBe 5L7I · UniProt Q99835 · UniProt P0ABE7
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