Research workbench
Structure of Prolyl Hydroxylase Domain-containing Protein (PHD) with Inhibitors
Analyse Structure of Prolyl Hydroxylase Domain-containing Protein (PHD) with Inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JZR
- Type
- protein
- Length
- 204 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Homo sapiens
- Molecule
- Egl nine homolog 1
- EC
- 1.14.11.29
- UniProt
- Q9GZT9
- Ligands
- 4JR, NI
- Pockets
- 1 · best druggability 0.64
Structure
x-ray diffraction · resolution 2.1 · 1 distinct chain · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Egl nine homolog 1 (EC 1.14.11.29) | protein | 204 | 27% helix, 30% strand | Q9GZT9 |
Ligands and binding sites
- 4JR · 2-(biphenyl-4-yl)-8-[(1-methyl-1H-imidazol-2-yl)methyl]-2,8-diazaspiro[4.5]decan-1-one · ligand · chains A
- NI · Nickel (II) ion · metal · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.64 | 0.87 | 23 | NI, 4JR, EDO |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4JZR · Structure of prolyl hydroxylase domain-containing protein (phd) with inhibitors · the same entry in another collection · chain A against A, TM-score 1.00
- Q9GZT9 · AlphaFold monomer V2.0 prediction for egl nine homolog 1 (Q9GZT9) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9GZT9
- Elsewhere: RCSB PDB 4JZR · PDBe 4JZR · UniProt Q9GZT9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.