Crystal structure of the VHL-EloC-EloB complex with a covalent compound bound to C77 of VHL. Determined by X-ray diffraction at 1.49 Å resolution. Released 26 Mar 2025.
Explore 9GIO in 3D Show helices and sheets RCSB PDB PDBe
9GIO contains 19 α-helices and 25 β-strands across 3 chains. 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 | 2-9 | 8 | 1 |
| β-strand | 10 | 1 | 2 |
| β-strand | 12-19 | 8 | 1 |
| β-strand | 23 | 1 | 3 |
| α-helix | 24-35 | 12 | |
| α-helix | 39-41 | 3 | |
| β-strand | 42-46 | 5 | 1 |
| β-strand | 49-50 | 2 | 1 |
| α-helix | 51-52 | 2 | |
| β-strand | 56 | 1 | 3 |
| α-helix | 57-60 | 4 | |
| β-strand | 68 | 1 | 4 |
| β-strand | 71 | 1 | 4 |
| α-helix | 72 | 1 | |
| β-strand | 73-79 | 7 | 1 |
| α-helix | 85-88 | 4 | |
| β-strand | 90 | 1 | 2 |
| α-helix | 91-100 | 10 | |
| α-helix | 101-103 | 3 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 18-22 | 5 | 1 |
| β-strand | 28-32 | 5 | 1 |
| α-helix | 33-36 | 4 | |
| α-helix | 40-46 | 7 | |
| β-strand | 59-61 | 3 | 1 |
| α-helix | 67-83 | 17 | |
| α-helix | 89-94 | 6 | |
| α-helix | 97-110 | 14 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 71-79 | 9 | 5 |
| α-helix | 83 | 1 | |
| β-strand | 84-89 | 6 | 6 |
| β-strand | 95-97 | 3 | 6 |
| β-strand | 101 | 1 | 6 |
| β-strand | 106-112 | 7 | 5 |
| β-strand | 116-121 | 6 | 6 |
| β-strand | 127 | 1 | 6 |
| β-strand | 129-130 | 2 | 5 |
| β-strand | 133 | 1 | 5 |
| β-strand | 136 | 1 | 6 |
| α-helix | 145-146 | 2 | |
| β-strand | 147-152 | 6 | 5 |
| α-helix | 158-169 | 12 | |
| α-helix | 172-177 | 6 | |
| α-helix | 182-189 | 8 | |
| α-helix | 194-205 | 12 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Elongin-B | A | protein | 107 | Homo sapiens | Q15370 (AlphaFold model) |
| Isoform 2 of Elongin-C | B | protein | 96 | Homo sapiens | Q15369 (AlphaFold model) |
| von Hippel-Lindau disease tumor suppressor | C | protein | 160 | Homo sapiens | P40337 (AlphaFold model) |
>9GIO_1 Elongin-B (chains A) GSHMDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTL GECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK
>9GIO_2 Isoform 2 of Elongin-C (chains B) MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC
>9GIO_3 von Hippel-Lindau disease tumor suppressor (chains C) MEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYR GHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPE NYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD
| ID | Name | Formula | Copies |
|---|---|---|---|
| 3JF | N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl… | C24 H32 N4 O4 S | 1 |
| A1IMD | N-[2-(dimethylsulfamoyl)-5-[(1-methylpyrazol-4-yl)methoxy]phenyl]propanamide | C16 H22 N4 O4 S | 1 |
Discovery of a Series of Covalent Ligands That Bind to Cys77 of the Von Hippel-Lindau Tumor Suppressor Protein (VHL). Lucas, S.C.C., Xu, Y., Hewitt, S. et al. ACS Med Chem Lett (2025) 16:693-699. DOI 10.1021/acsmedchemlett.4c00582 · PubMed
Other PDB entries of the same protein (UniProt Q15370 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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