Research workbench
Crystal structure of inhibitor jnj-36689282 in complex with prefusion rsv F glycoprotein
Analyse Crystal structure of inhibitor jnj-36689282 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
- 6VKD
- Type
- protein
- Length
- 441 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prefusion rsv F (ds-CAV1)
- UniProt
- W8RJF9, M1E1E4
- Ligands
- R0P, SO4, CL
- Pockets
- 2 · best druggability 0.30
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Prefusion rsv F (ds-CAV1) | protein | 441 | 31% helix, 34% strand | W8RJF9, M1E1E4 |
Ligands and binding sites
- R0P · 1-cyclopropyl-3-({1-[3-(methylsulfonyl)propyl]-1H-pyrrolo[3,2-c]pyridin-2-yl}methyl)-1,3-dihydro-2H-imidazo[4,5-c]pyridin-2-one · ligand · chains F
- SO4 · Sulfate ion · ion · 6 copies · chains F
- CL · Chloride ion · ion · 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 | 57 | 0.30 | 0.75 | 15 | empty |
| 2 | 53 | 0.27 | 0.75 | 13 | empty |
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 6VKD · Crystal Structure of Inhibitor JNJ-36689282 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 6VKD · PDBe 6VKD · UniProt W8RJF9 · UniProt M1E1E4
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