MolNFT v1 · #118941 · protein
Crystal structure of the fifth bromodomain of human PB1 in complex with compound 28
5FH8 · Protein polybromo-1: “Crystal structure of the fifth bromodomain of human PB1 in complex with compound 28”. X-ray diffraction, 1 ligand (5XK), 7 pockets (best druggability 0.76). MolNFT v1 #118941 on GenesisL1: 3D structure, binding…
- PDB
- 5FH8
- Type
- protein
- Length
- 441 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein polybromo-1
- UniProt
- Q86U86
- Ligands
- 5XK
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein polybromo-1 | protein | 112 | 63% helix, 2% strand | Q86U86 |
| B | Protein polybromo-1 | protein | 111 | 62% helix, 2% strand | Q86U86 |
| C, D | Protein polybromo-1 | protein | 109 | 65% helix, 2% strand | Q86U86 |
Ligands and binding sites
- 5XK · 6-chloranyl-3-(2-ethylbutyl)-4~{H}-pyrrolo[1,2-a]quinazolin-5-one · ligand · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · chains A
- EDO · 1,2-ethanediol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.76 | 0.82 | 59 | 5XK |
| 2 | 465 | 0.68 | 0.79 | 50 | empty |
| 3 | 445 | 0.62 | 0.76 | 41 | empty |
| 4 | 58 | 0.48 | 0.84 | 15 | 5XK |
| 5 | 202 | 0.46 | 0.74 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–C · 710 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 425 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 192 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 155 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5FH8 · Crystal structure of the fifth bromodomain of human PB1 in complex with compound 28 · the same entry in another collection · chain A against A, TM-score 1.00
- Q86U86 · AlphaFold monomer V2.0 prediction for protein polybromo-1 (Q86U86) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q86U86
- Elsewhere: RCSB PDB 5FH8 · PDBe 5FH8 · UniProt Q86U86
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