Research workbench
Crystal structure of inhibitor jnj-53718678 in complex with prefusion rsv F glycoprotein
Analyse Crystal structure of inhibitor jnj-53718678 in complex with prefusion rsv F… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KWW
- Type
- protein
- Length
- 428 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion glycoprotein F0, envelope glycoprotein chimera
- UniProt
- W8RJF9, M1E1E4
- Ligands
- 6YA, NAG, SO4
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Fusion glycoprotein F0, envelope glycoprotein chimera | protein | 428 | 30% helix, 35% strand | W8RJF9, M1E1E4 |
Ligands and binding sites
- 6YA · 3-[[5-chloranyl-1-(3-methylsulfonylpropyl)indol-2-yl]methyl]-1-[2,2,2-tris(fluoranyl)ethyl]imidazo[4,5-c]pyridin-2-one · ligand · chains F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains F
- SO4 · Sulfate ion · ion · 10 copies · chains F
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.45 | 0.76 | 32 | empty |
| 2 | 69 | 0.31 | 0.75 | 16 | SO4 |
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5KWW · Crystal Structure of Inhibitor JNJ-53718678 In Complex with Prefusion RSV F Glycoprotein · the same entry in another collection · chain F against F, TM-score 1.00
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 W8RJF9
- Every structure of UniProt M1E1E4
- Elsewhere: RCSB PDB 5KWW · PDBe 5KWW · UniProt W8RJF9 · UniProt M1E1E4
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