MolNFT v1 · #117504 · protein
Crystal structure of inhibitor jnj-2408068 in complex with prefusion rsv F glycoprotein
5EA3 · Fusion glycoprotein F0: “Crystal structure of inhibitor jnj-2408068 in complex with prefusion rsv F glycoprotein”. X-ray diffraction, 2 ligands (5NK, SO4), 3 pockets (best druggability 0.29). MolNFT v1 #117504 on GenesisL1: 3D…
- PDB
- 5EA3
- Type
- protein
- Length
- 419 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion glycoprotein F0
- UniProt
- P03420
- Ligands
- 5NK, SO4
- Pockets
- 3 · best druggability 0.29
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Fusion glycoprotein F0 | protein | 419 | 31% helix, 37% strand | P03420 |
Ligands and binding sites
- 5NK · 2-[[2-[[1-(2-azanylethyl)piperidin-4-yl]amino]-4-methyl-benzimidazol-1-yl]methyl]-6-methyl-pyridin-3-ol · ligand · chains F
- SO4 · Sulfate ion · ion · 6 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
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.29 | 0.75 | 13 | empty |
| 2 | 57 | 0.27 | 0.73 | 15 | empty |
| 3 | 52 | 0.27 | 0.74 | 13 | empty |
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 5EA3 · Crystal Structure of Inhibitor JNJ-2408068 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 P03420
- Elsewhere: RCSB PDB 5EA3 · PDBe 5EA3 · UniProt P03420
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