Research workbench
Crystal structure of BCL-xl in complex with a quinazoline sulfonamide inhibitor
Analyse Crystal structure of BCL-xl in complex with a quinazoline sulfonamide inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QKD
- Type
- protein
- Length
- 282 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BCL-2-like protein 1
- UniProt
- Q07817
- Ligands
- HI0, CL
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BCL-2-like protein 1 | protein | 140 | 79% helix, 0% strand | Q07817 |
| B | BCL-2-like protein 1 | protein | 142 | 77% helix, 0% strand | Q07817 |
Ligands and binding sites
- HI0 · (R)-N-(7-(4-((4'-chlorobiphenyl-2-yl)methyl)piperazin-1-yl)quinazolin-4-yl)-4-(4-(dimethylamino)-1-(phenylthio)butan-2-ylamino)-3-nitrobenzenesulfonamide · 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 | 164 | 0.58 | 0.82 | 30 | empty |
| 2 | 128 | 0.48 | 0.78 | 16 | HI0 |
| 3 | 114 | 0.47 | 0.78 | 15 | empty |
| 4 | 76 | 0.42 | 0.80 | 18 | empty |
| 5 | 52 | 0.28 | 0.74 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 508 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3QKD · Crystal structure of Bcl-xL in complex with a Quinazoline sulfonamide inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q07817 · AlphaFold monomer V2.0 prediction for BCL-2-like protein 1 (Q07817) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 3QKD · PDBe 3QKD · UniProt Q07817
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