MolNFT v1 · #118904 · protein
Crystal structure of the bromodomain of human BRPF1 in complex with pfi-4 chemical probe
5FG5 · Peregrin: “Crystal structure of the bromodomain of human BRPF1 in complex with pfi-4 chemical probe”. X-ray diffraction, 2 ligands (5XF, NO3), 4 pockets (best druggability 0.75). MolNFT v1 #118904 on GenesisL1: 3D structure, binding…
- PDB
- 5FG5
- Type
- protein
- Length
- 222 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peregrin
- UniProt
- P55201
- Ligands
- 5XF, NO3
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peregrin | protein | 114 | 63% helix, 0% strand | P55201 |
| B | Peregrin | protein | 108 | 65% helix, 0% strand | P55201 |
Ligands and binding sites
- 5XF · ~{N}-(1,3-dimethyl-2-oxidanylidene-6-pyrrolidin-1-yl-benzimidazol-5-yl)-2-methoxy-benzamide · ligand · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.75 | 0.82 | 52 | empty |
| 2 | 72 | 0.49 | 0.83 | 16 | 5XF |
| 3 | 67 | 0.47 | 0.83 | 17 | 5XF |
| 4 | 59 | 0.28 | 0.74 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 638 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5FG5 · Crystal structure of the bromodomain of human BRPF1 in complex with PFI-4 chemical probe · the same entry in another collection · chain A against A, TM-score 1.00
- P55201 · AlphaFold monomer V2.0 prediction for peregrin (P55201) · a predicted model of the same protein · chain B 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 P55201
- Elsewhere: RCSB PDB 5FG5 · PDBe 5FG5 · UniProt P55201
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