Research workbench
Crystal structure of BCL-xl bound to compound 13: (R)-2-(3-([1,1'- biphenyl]-4-carbonyl)-3-(4-METHYLBENZYL)UREIDO)-3-(((3R,5R,7R)- adamantan-1-YLMETHYL)SULFONYL)PROPANOIC acid
Analyse Crystal structure of BCL-xl bound to compound 13: (R)-2-(3-([1,1'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UVG
- Type
- protein
- Length
- 1,684 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BCL-2-like protein 1
- UniProt
- Q07817
- Ligands
- QHP, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 11 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BCL-2-like protein 1 | protein | 145 | 76% helix, 0% strand | Q07817 |
| B | BCL-2-like protein 1 | protein | 144 | 76% helix, 0% strand | Q07817 |
| C | BCL-2-like protein 1 | protein | 138 | 76% helix, 0% strand | Q07817 |
| D | BCL-2-like protein 1 | protein | 140 | 78% helix, 0% strand | Q07817 |
| E | BCL-2-like protein 1 | protein | 140 | 77% helix, 0% strand | Q07817 |
| F | BCL-2-like protein 1 | protein | 141 | 77% helix, 0% strand | Q07817 |
| G | BCL-2-like protein 1 | protein | 141 | 77% helix, 0% strand | Q07817 |
| H, K | BCL-2-like protein 1 | protein | 142 | 77% helix, 0% strand | Q07817 |
| I | BCL-2-like protein 1 | protein | 138 | 77% helix, 0% strand | Q07817 |
| J | BCL-2-like protein 1 | protein | 133 | 78% helix, 0% strand | Q07817 |
| L | BCL-2-like protein 1 | protein | 140 | 75% helix, 0% strand | Q07817 |
Ligands and binding sites
- QHP · (R)-2-(3-([1,1'-Biphenyl]-4-carbonyl)-3-(4-methylbenzyl)ureido)-3-(((3R,5R,7R)-adamantan-1-ylmethyl)sulfonyl)propanoic acid · ligand · 12 copies · chains A, B, C, K, D, E, F, G, H, I, J, L
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, G, H, C, D, I, J, K, L
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 926 | 0.83 | 0.85 | 96 | QHP |
| 2 | 613 | 0.72 | 0.80 | 55 | EDO, SO4 |
| 3 | 499 | 0.71 | 0.80 | 40 | SO4 |
| 4 | 332 | 0.67 | 0.82 | 50 | empty |
| 5 | 241 | 0.63 | 0.82 | 41 | EDO |
Interfaces
20 interfaces between chains.
- A–B · 2318 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 2281 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2240 Ų buried · 29 hydrogen bonds · protein-protein
- K–L · 2214 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 2145 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6UVG · Crystal structure of BCL-XL bound to compound 13… · the same entry in another collection · chain L against L, 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 Q07817
- Elsewhere: RCSB PDB 6UVG · PDBe 6UVG · UniProt Q07817
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