MolNFT v1 · #166605 · protein
Crystal structure of BCL-xl bound to compound 12: (R)-2-(3-([1,1'- biphenyl]-4-carbonyl)-3-(4-METHYLBENZYL)UREIDO)-3- ((CYCLOHEXYLMETHYL)SULFONYL)PROPANOIC acid
6UVF · BCL-2-like protein 1: “Crystal structure of BCL-xl bound to compound 12: (R)-2-(3-([1,1'…”. X-ray diffraction, 2 ligands (QHS, SO4), 20 pockets (best druggability 0.82). MolNFT v1 #166605 on GenesisL1: 3D structure, binding sites…
- PDB
- 6UVF
- Type
- protein
- Length
- 1,704 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BCL-2-like protein 1
- UniProt
- Q07817
- Ligands
- QHS, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 9 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BCL-2-like protein 1 | protein | 145 | 75% helix, 0% strand | Q07817 |
| B, D | BCL-2-like protein 1 | protein | 144 | 76% helix, 0% strand | Q07817 |
| C, H | BCL-2-like protein 1 | protein | 142 | 77% helix, 0% strand | Q07817 |
| E, G | BCL-2-like protein 1 | protein | 139 | 76% helix, 0% strand | Q07817 |
| F | BCL-2-like protein 1 | protein | 140 | 77% helix, 0% strand | Q07817 |
| I | BCL-2-like protein 1 | protein | 138 | 76% helix, 0% strand | Q07817 |
| J | BCL-2-like protein 1 | protein | 144 | 76% helix, 0% strand | Q07817 |
| K | BCL-2-like protein 1 | protein | 147 | 78% helix, 0% strand | Q07817 |
| L | BCL-2-like protein 1 | protein | 140 | 77% helix, 0% strand | Q07817 |
Ligands and binding sites
- QHS · (R)-2-(3-([1,1'-biphenyl]-4-carbonyl)-3-(4-methylbenzyl)ureido)-3-((cyclohexylmethyl)sulfonyl) propanoic acid · ligand · 12 copies · chains A, B, D, C, K, E, F, I, G, H, J, L
- SO4 · Sulfate ion · ion · 22 copies · chains A, B, C, D, F, E, G, H, I, J, K, L
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, D, K, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.82 | 0.83 | 88 | QHS |
| 2 | 1138 | 0.81 | 0.82 | 100 | QHS |
| 3 | 870 | 0.73 | 0.78 | 69 | EDO, QHS |
| 4 | 956 | 0.73 | 0.77 | 94 | SO4, EDO |
| 5 | 1081 | 0.73 | 0.76 | 109 | SO4 |
Interfaces
26 interfaces between chains.
- A–B · 2356 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2283 Ų buried · 31 hydrogen bonds · protein-protein
- I–J · 2242 Ų buried · 29 hydrogen bonds · protein-protein
- G–H · 2190 Ų buried · 28 hydrogen bonds · protein-protein
- K–L · 2161 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6UVF · Crystal structure of BCL-XL bound to compound 12… · 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 6UVF · PDBe 6UVF · UniProt Q07817
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