HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with a Spiro[4.5]decanone inhibitor (JPHM-2-167). Determined by X-ray diffraction at 1.4 Å resolution. Released 5 Feb 2020.
Explore 6QGV in 3D Show helices and sheets RCSB PDB PDBe
6QGV contains 8 α-helices and 15 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 |
|---|---|---|---|
| α-helix | 190-193 | 4 | |
| α-helix | 194-198 | 5 | |
| α-helix | 199-205 | 7 | |
| β-strand | 207-210 | 4 | 1 |
| α-helix | 216-228 | 13 | |
| β-strand | 255-259 | 5 | 1 |
| α-helix | 267-281 | 15 | |
| β-strand | 292-295 | 4 | 1 |
| α-helix | 296-297 | 2 | |
| β-strand | 298-303 | 6 | 1 |
| β-strand | 310-313 | 4 | 2 |
| β-strand | 322-329 | 8 | 1 |
| β-strand | 331 | 1 | 3 |
| α-helix | 336-339 | 4 | |
| β-strand | 340 | 1 | 4 |
| β-strand | 343-345 | 3 | 2 |
| β-strand | 354-356 | 3 | 2 |
| β-strand | 359 | 1 | 3 |
| β-strand | 363-367 | 5 | 1 |
| β-strand | 374-376 | 3 | 2 |
| β-strand | 379 | 1 | 4 |
| β-strand | 383-392 | 10 | 1 |
| α-helix | 393-400 | 8 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Egl nine homolog 1 | A | protein | 233 | Homo sapiens | Q9GZT9 (AlphaFold model) |
>6QGV_1 Egl nine homolog 1 (chains A) GSHMASPNGQTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGK FTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKING RTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFA DIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLTGE
| ID | Name | Formula | Copies |
|---|---|---|---|
| IPA | Isopropyl alcohol | C3 H8 O | 1 |
| J2H | 8-[(3-methylpyridin-2-yl)methyl]-3-(4-phenylphenyl)-1-pyrimidin-2-yl-1,3,8-tria… | C30 H28 N6 O2 | 1 |
| MN | Manganese (II) ion | Mn | 1 |
Water and common crystallization additives (SO4, GOL) are not listed.
Studies on spiro[4.5]decanone prolyl hydroxylase domain inhibitors. Holt-Martyn, J.P., Tumber, A., Rahman, M.Z. et al. Medchemcomm (2019) 10:500-504. DOI 10.1039/c8md00548f · PubMed
Other PDB entries of the same protein (UniProt Q9GZT9 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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