Research workbench
Crystal structure of BCL-xl in complex with abt-737
Analyse Crystal structure of BCL-xl in complex with abt-737 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YXJ
- Type
- protein
- Length
- 279 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apoptosis regulator BCL-X
- UniProt
- Q07817
- Ligands
- N3C, CL
- Pockets
- 5 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apoptosis regulator BCL-X | protein | 137 | 76% helix, 0% strand | Q07817 |
| B | Apoptosis regulator BCL-X | protein | 142 | 77% helix, 0% strand | Q07817 |
Ligands and binding sites
- N3C · 4-{4-[(4'-chlorobiphenyl-2-yl)methyl]piperazin-1-yl}-N-{[4-({(1R)-3-(dimethylamino)-1-[(phenylthio) methyl]propyl}amino)-3-nitrophenyl]sulfonyl}benzamide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.53 | 0.81 | 24 | empty |
| 2 | 118 | 0.46 | 0.78 | 14 | empty |
| 3 | 116 | 0.46 | 0.78 | 19 | empty |
| 4 | 88 | 0.45 | 0.80 | 18 | empty |
| 5 | 55 | 0.29 | 0.74 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 496 Ų buried · 5 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 Q07817
- Elsewhere: RCSB PDB 2YXJ · PDBe 2YXJ · UniProt Q07817
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