Research workbench
Crystal structure of the human BRPF1 bromodomain in complex with BZ135
Analyse Crystal structure of the human BRPF1 bromodomain in complex with BZ135 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O4S
- Type
- protein
- Length
- 223 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peregrin
- UniProt
- P55201
- Ligands
- 9KW, 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 | 112 | 64% helix, 0% strand | P55201 |
| B | Peregrin | protein | 111 | 64% helix, 0% strand | P55201 |
Ligands and binding sites
- 9KW · ~{N}-[1,4-dimethyl-7-morpholin-4-yl-2,3-bis(oxidanylidene)quinoxalin-6-yl]-5,6,7,8-tetrahydronaphthalene-2-sulfonamide · 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 | 636 | 0.75 | 0.81 | 56 | NO3 |
| 2 | 82 | 0.47 | 0.81 | 19 | 9KW |
| 3 | 79 | 0.47 | 0.81 | 19 | 9KW |
| 4 | 136 | 0.39 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 644 Ų buried · 19 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 5O4S · PDBe 5O4S · UniProt P55201
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