MolNFT v1 · #104869 · protein
Crystal structure analysis of full-length BCL-xl in complex with the inhibitor abt-263
4QNQ · BCL-2-like protein 1: “Crystal structure analysis of full-length BCL-xl in complex with the inhibitor abt-263”. X-ray diffraction, 1 ligand (1XJ), 20 pockets (best druggability 0.85). MolNFT v1 #104869 on GenesisL1: 3D structure…
- PDB
- 4QNQ
- Type
- protein
- Length
- 1,733 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BCL-2-like protein 1
- UniProt
- P53563
- Ligands
- 1XJ
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 10 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BCL-2-like protein 1 | protein | 144 | 78% helix, 0% strand | P53563 |
| B | BCL-2-like protein 1 | protein | 144 | 77% helix, 0% strand | P53563 |
| C | BCL-2-like protein 1 | protein | 144 | 75% helix, 0% strand | P53563 |
| D | BCL-2-like protein 1 | protein | 141 | 78% helix, 0% strand | P53563 |
| E | BCL-2-like protein 1 | protein | 148 | 74% helix, 0% strand | P53563 |
| F, J | BCL-2-like protein 1 | protein | 149 | 77% helix, 0% strand | P53563 |
| G | BCL-2-like protein 1 | protein | 140 | 79% helix, 0% strand | P53563 |
| H, L | BCL-2-like protein 1 | protein | 142 | 78% helix, 0% strand | P53563 |
| I | BCL-2-like protein 1 | protein | 147 | 76% helix, 0% strand | P53563 |
| K | BCL-2-like protein 1 | protein | 143 | 80% helix, 0% strand | P53563 |
Ligands and binding sites
- 1XJ · 4-(4-{[2-(4-chlorophenyl)-5,5-dimethylcyclohex-1-en-1-yl]methyl}piperazin-1-yl)-N-[(4-{[(2R)-4-(morpholin-4-yl)-1-(phenylsulfanyl)butan-2-yl]amino}-3-[(trifluoromethyl)sulfonyl]phenyl)sulfonyl]benzamide · ligand · 12 copies · chains A, B, C, G, D, J, E, F, I, H, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.85 | 0.86 | 81 | 1XJ |
| 2 | 984 | 0.83 | 0.84 | 86 | 1XJ |
| 3 | 1192 | 0.81 | 0.82 | 115 | 1XJ |
| 4 | 722 | 0.79 | 0.83 | 64 | 1XJ |
| 5 | 838 | 0.77 | 0.80 | 63 | 1XJ |
Interfaces
19 interfaces between chains.
- B–H · 760 Ų buried · 5 hydrogen bonds · protein-protein
- G–I · 564 Ų buried · 7 hydrogen bonds · protein-protein
- H–J · 540 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 503 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 479 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4QNQ · Crystal Structure Analysis of full-length Bcl-XL in complex with the inhibitor ABT-263 · 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 P53563
- Elsewhere: RCSB PDB 4QNQ · PDBe 4QNQ · UniProt P53563
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