MolNFT v1 · #117103 · protein
Crystal structure of the human BRPF1 bromodomain in complex with SEED5
5DYA · Peregrin: “Crystal structure of the human BRPF1 bromodomain in complex with SEED5”. X-ray diffraction, 2 ligands (5GV, NO3), 1 pocket (best druggability 0.52). MolNFT v1 #117103 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5DYA
- Type
- protein
- Length
- 112 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peregrin
- UniProt
- P55201
- Ligands
- 5GV, NO3
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peregrin | protein | 112 | 65% helix, 0% strand | P55201 |
Ligands and binding sites
- 5GV · (2R)-2-ethyl-3-oxo-1,2,3,4-tetrahydroquinoxaline-6-carboxylic acid · ligand · chains A
- NO3 · Nitrate ion · ion · 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 | 88 | 0.52 | 0.83 | 16 | 5GV |
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 P55201
- Elsewhere: RCSB PDB 5DYA · PDBe 5DYA · UniProt P55201
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