Research workbench
Crystal structure analysis of pp-BRD20 from TB427TMP complexed with bi-2536
Analyse Crystal structure analysis of pp-BRD20 from TB427TMP complexed with bi-2536 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C8G
- Type
- protein
- Length
- 239 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pp-BRD20
- UniProt
- D0A8L1
- Ligands
- R78, UNX
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pp-BRD20 | protein | 122 | 61% helix, 0% strand | D0A8L1 |
| B | Pp-BRD20 | protein | 117 | 67% helix, 0% strand | D0A8L1 |
Ligands and binding sites
- R78 · 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide · ligand · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.67 | 0.78 | 55 | empty |
| 2 | 145 | 0.53 | 0.80 | 23 | R78, UNX |
Interfaces
1 interface between chains.
- A–B · 240 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5C8G · Crystal Structure Analysis of PP-BRD20 from Tb427tmp complexed with BI-2536 · the same entry in another collection · chain A against A, TM-score 1.00
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 D0A8L1
- Elsewhere: RCSB PDB 5C8G · PDBe 5C8G · UniProt D0A8L1
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