MolNFT v1 · #87575 · protein
Crystal structure of BCL-xl in complex with benzoylurea compound (42)
4C5D · BCL-2-like protein 1: “Crystal structure of BCL-xl in complex with benzoylurea compound (42)”. X-ray diffraction, 2 ligands (X0R, SO4), 6 pockets (best druggability 0.67). MolNFT v1 #87575 on GenesisL1: 3D structure, binding sites…
- PDB
- 4C5D
- Type
- protein
- Length
- 290 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BCL-2-like protein 1
- UniProt
- Q07817
- Ligands
- X0R, SO4
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BCL-2-like protein 1 | protein | 145 | 70% helix, 0% strand | Q07817 |
| B | BCL-2-like protein 1 | protein | 145 | 76% helix, 0% strand | Q07817 |
Ligands and binding sites
- X0R · (R)-3-(4-bromobenzylthio)-2-(3-(3-((2,4-difluorophenyl)ethynyl)benzoyl)-3-propylureido)propanoic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.67 | 0.80 | 54 | SO4, EDO |
| 2 | 93 | 0.59 | 0.86 | 17 | X0R |
| 3 | 70 | 0.54 | 0.86 | 16 | X0R |
| 4 | 50 | 0.36 | 0.80 | 14 | empty |
| 5 | 62 | 0.31 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2421 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 4C5D · Crystal structure of Bcl-xL in complex with benzoylurea compound (42) · the same entry in another collection · chain B against B, 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 A against A, TM-score 0.73
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 4C5D · PDBe 4C5D · UniProt Q07817
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