MolNFT v1 · #164287 · protein
Hif prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 4-hydroxy-N-(4- phenoxybenzyl)-2-(1H-pyrazol-1-YL)PYRIMIDINE-5-carboxamide
6ST3 · Egl nine homolog 1: “Hif prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 4-hydroxy-N-(4…”. X-ray diffraction, 2 ligands (LUW, MN), 4 pockets (best druggability 0.63). MolNFT v1 #164287 on GenesisL1: 3D structure, binding sites…
- PDB
- 6ST3
- Type
- protein
- Length
- 419 residues
- Chains
- 2
- 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
- LUW, MN
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Egl nine homolog 1 (EC 1.14.11.29) | protein | 210 | 30% helix, 30% strand | Q9GZT9 |
| B | Egl nine homolog 1 (EC 1.14.11.29) | protein | 209 | 31% helix, 32% strand | Q9GZT9 |
Ligands and binding sites
- LUW · 4-oxidanyl-~{N}-[(4-phenoxyphenyl)methyl]-2-pyrazol-1-yl-pyrimidine-5-carboxamide · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.63 | 0.89 | 21 | LUW, FMT |
| 2 | 98 | 0.62 | 0.88 | 22 | MN, LUW, FMT |
| 3 | 470 | 0.61 | 0.75 | 42 | empty |
| 4 | 102 | 0.36 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 304 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 6ST3 · PDBe 6ST3 · UniProt Q9GZT9
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