MolNFT v1 · #129798 · protein
Crystal structure of the human BRPF1 bromodomain in complex with BZ097
5OV8 · Peregrin: “Crystal structure of the human BRPF1 bromodomain in complex with BZ097”. X-ray diffraction, 2 ligands (AXN, NO3), 4 pockets (best druggability 0.76). MolNFT v1 #129798 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5OV8
- Type
- protein
- Length
- 222 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peregrin
- UniProt
- P55201
- Ligands
- AXN, NO3
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peregrin | protein | 111 | 65% helix, 0% strand | P55201 |
Ligands and binding sites
- AXN · ~{N}-[1,4-dimethyl-2,3-bis(oxidanylidene)-7-pyrrolidin-1-yl-quinoxalin-6-yl]-4-(2-methylpropyl) benzenesulfonamide · ligand · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.76 | 0.83 | 57 | NO3 |
| 2 | 83 | 0.48 | 0.82 | 19 | AXN |
| 3 | 72 | 0.47 | 0.82 | 19 | AXN |
| 4 | 80 | 0.34 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 625 Ų buried · 11 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 P55201
- Elsewhere: RCSB PDB 5OV8 · PDBe 5OV8 · UniProt P55201
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