MolNFT v1 · #171177 · protein
Hif prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with bicyclic bb-287
6YVX · Egl nine homolog 1: “Hif prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with bicyclic bb-287”. X-ray diffraction, 3 ligands (2JP, BCT, MN), 1 pocket (best druggability 0.64). MolNFT v1 #171177 on GenesisL1: 3D structure, binding…
- PDB
- 6YVX
- Type
- protein
- Length
- 225 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Egl nine homolog 1
- EC
- 1.14.11.29
- UniProt
- Q9GZT9
- Ligands
- 2JP, BCT, MN
- Pockets
- 1 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Egl nine homolog 1 (EC 1.14.11.29) | protein | 225 | 29% helix, 30% strand | Q9GZT9 |
Ligands and binding sites
- 2JP · 4-(isoquinolin-3-ylamino)-4-oxobutanoic acid · ligand · chains A
- BCT · Bicarbonate ion · ligand · chains A
- MN · Manganese (II) ion · metal · 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 | 122 | 0.64 | 0.87 | 21 | MN, 2JP |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6YVX · HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with bicyclic BB-287 · 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 0.91
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 6YVX · PDBe 6YVX · UniProt Q9GZT9
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