Research workbench
First bromodomain from leishmania donovani LDBPK.091320 complexed with bi-2536
Analyse First bromodomain from leishmania donovani LDBPK.091320 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
- 5TCM
- Type
- protein
- Length
- 346 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- E9BA17
- Ligands
- R78
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 116 | 66% helix, 0% strand | E9BA17 |
| B, C | Uncharacterized protein | protein | 115 | 68% helix, 0% strand | E9BA17 |
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 · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 3 copies · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 795 | 0.75 | 0.79 | 55 | empty |
| 2 | 123 | 0.51 | 0.80 | 21 | R78 |
| 3 | 121 | 0.51 | 0.80 | 22 | R78 |
| 4 | 122 | 0.50 | 0.80 | 22 | R78 |
Interfaces
3 interfaces between chains.
- A–C · 519 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 498 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 495 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5TCM · First Bromodomain from Leishmania donovani LdBPK.091320 complexed with BI-2536 · the same entry in another collection · chain B against B, 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 E9BA17
- Elsewhere: RCSB PDB 5TCM · PDBe 5TCM · UniProt E9BA17
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