MolNFT v1 · #127503 · protein
Crystal structure of the bromodomain of human BRPF1 in complex with ni-57 chemical probe
5MYG · Peregrin: “Crystal structure of the bromodomain of human BRPF1 in complex with ni-57 chemical probe”. X-ray diffraction, 1 ligand (LS8), 6 pockets (best druggability 0.71). MolNFT v1 #127503 on GenesisL1: 3D structure, binding sites…
- PDB
- 5MYG
- Type
- protein
- Length
- 453 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peregrin
- UniProt
- P55201
- Ligands
- LS8
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peregrin | protein | 115 | 60% helix, 0% strand | P55201 |
| C | Peregrin | protein | 112 | 64% helix, 0% strand | P55201 |
| D | Peregrin | protein | 111 | 65% helix, 0% strand | P55201 |
Ligands and binding sites
- LS8 · 4-cyano-~{N}-(1,3-dimethyl-2-oxidanylidene-quinolin-6-yl)-2-methoxy-benzenesulfonamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.71 | 0.81 | 52 | empty |
| 2 | 383 | 0.66 | 0.79 | 50 | LS8 |
| 3 | 80 | 0.52 | 0.84 | 17 | LS8 |
| 4 | 84 | 0.49 | 0.82 | 19 | LS8 |
| 5 | 83 | 0.39 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 669 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 196 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 164 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5MYG · Crystal structure of the bromodomain of human BRPF1 in complex with NI-57 chemical probe · the same entry in another collection · chain D against D, TM-score 1.00
- P55201 · AlphaFold monomer V2.0 prediction for peregrin (P55201) · a predicted model of the same protein · chain D 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 5MYG · PDBe 5MYG · UniProt P55201
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