MolNFT v1 · #130827 · protein
Pandda analysis group deposition -- crystal structure of BRD1 in complex with N10128A
5PNX · Bromodomain-containing protein 1: “Pandda analysis group deposition -- crystal structure of BRD1 in complex with N10128A”. X-ray diffraction, 2 ligands (M3I, NA), 3 pockets (best druggability 0.54). MolNFT v1 #130827 on GenesisL1…
- PDB
- 5PNX
- Type
- protein
- Length
- 246 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 1
- UniProt
- O95696
- Ligands
- M3I, NA
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bromodomain-containing protein 1 | protein | 123 | 68% helix, 0% strand | O95696 |
Ligands and binding sites
- M3I · 5-methyl-1,2-oxazol-3-amine · ligand · chains A
- NA · Sodium ion · metal · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.54 | 0.75 | 32 | empty |
| 2 | 98 | 0.49 | 0.81 | 16 | EDO, M3I |
| 3 | 77 | 0.48 | 0.82 | 17 | EDO |
Interfaces
1 interface between chains.
- A–B · 536 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 5PNX · PanDDA analysis group deposition -- Crystal Structure of BRD1 in complex with N10128a · the same entry in another collection · chain A against A, TM-score 1.00
- O95696 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 1 (O95696) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 O95696
- Elsewhere: RCSB PDB 5PNX · PDBe 5PNX · UniProt O95696
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