Crystal Structure of Inhibitor JNJ-36689282 in Complex with Prefusion RSV F Glycoprotein. Determined by X-ray diffraction at 2.5 Å resolution. Released 27 May 2020.
Explore 6VKD in 3D Show helices and sheets RCSB PDB PDBe
6VKD contains 19 α-helices and 24 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 29-33 | 5 | 1 |
| β-strand | 38-60 | 23 | 1 |
| α-helix | 74-96 | 23 | |
| α-helix | 139-141 | 3 | |
| α-helix | 149-158 | 10 | |
| α-helix | 163-170 | 8 | |
| β-strand | 176-180 | 5 | 1 |
| β-strand | 186-194 | 9 | 1 |
| α-helix | 195-198 | 4 | |
| α-helix | 199-203 | 5 | |
| α-helix | 204-208 | 5 | |
| α-helix | 217-239 | 23 | |
| β-strand | 243-244 | 2 | 1 |
| α-helix | 254-263 | 10 | |
| α-helix | 268-275 | 8 | |
| α-helix | 278-283 | 6 | |
| β-strand | 286-293 | 8 | 1 |
| β-strand | 296-318 | 23 | 1 |
| β-strand | 321-322 | 2 | 2 |
| β-strand | 333-336 | 4 | 2 |
| β-strand | 340-345 | 6 | 1 |
| β-strand | 348-352 | 5 | 1 |
| α-helix | 355-357 | 3 | |
| β-strand | 359-361 | 3 | 1 |
| β-strand | 364-368 | 5 | 1 |
| α-helix | 369-371 | 3 | |
| β-strand | 373-375 | 3 | 1 |
| α-helix | 377-380 | 4 | |
| α-helix | 381-384 | 4 | |
| β-strand | 394-398 | 5 | 2 |
| β-strand | 404-407 | 4 | 3 |
| β-strand | 411-416 | 6 | 3 |
| β-strand | 422-426 | 5 | 4 |
| β-strand | 430-434 | 5 | 4 |
| α-helix | 435-436 | 2 | |
| β-strand | 438-443 | 6 | 3 |
| β-strand | 449-452 | 4 | 4 |
| β-strand | 455-458 | 4 | 4 |
| α-helix | 459-460 | 2 | |
| β-strand | 465-469 | 5 | 1 |
| α-helix | 474-477 | 4 | |
| β-strand | 487-491 | 5 | 2 |
| α-helix | 492-504 | 13 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Prefusion RSV F (DS-Cav1) | F | protein | 568 | Human respiratory syncytial virus, Human immunodeficiency virus 1 | M1E1E4 (AlphaFold model), P03420 |
>6VKD_1 Prefusion RSV F (DS-Cav1) (chains F) MELLILKANAITTILTAVTFCFASGQNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIE LSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQSTPATNNRARRELPRFMNYTLN NAKKTNVTLSKKRKRRFLGFLLGVGSAIASGVAVCKVLHLEGEVNKIKSALLSTNKAVVS LSNGVSVLTFKVLDLKNYIDKQLLPILNKQSCSISNIETVIEFQQKNNRLLEITREFSVN AGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMCIIKEEVLAYV VQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKV QSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKT KCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDP LVFPSDEFDASISQVNEKINQSLAFIRKSDELLSAIGGYIPEAPRDGQAYVRKDGEWVLL STFLGGLVPRGSHHHHHHSAWSHPQFEK
| ID | Name | Formula | Copies |
|---|---|---|---|
| R0P | 1-cyclopropyl-3-({1-[3-(methylsulfonyl)propyl]-1H-pyrrolo[3,2-c]pyridin-2-yl}me… | C21 H23 N5 O3 S | 1 |
Water and common crystallization additives (SO4, CL) are not listed.
Discovery of 3-({5-Chloro-1-[3-(methylsulfonyl)propyl]-1H-indol-2-yl}methyl)-1-(2,2,2-trifluoroethyl)-1,3-dihydro-2H-imidazo[4,5-c]pyridin-2-one (JNJ-53718678), a Potent and Orally Bioavailable Fusion Inhibitor of Respiratory Syncytial Virus. Vendeville, S., Tahri, A., Hu, L. et al. J Med Chem (2020) 63:8046-8058. DOI 10.1021/acs.jmedchem.0c00226 · PubMed
Other PDB entries of the same protein (UniProt M1E1E4 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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