Research workbench

Crystal structure of BCL-xl in complex with compound 10

Analyse Crystal structure of BCL-xl in complex with compound 10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WIZ
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: LC6, PO4
Pockets: 6 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain · 80% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	BCL-2-like protein 1	protein	141	80% helix, 1% strand	Q07817

Ligands and binding sites

LC6 · 7-(4-{[(4-{[(2R)-4-(dimethylamino)-1-(phenylsulfanyl)butan-2-yl]amino}-3-nitrophenyl)sulfonyl]carbamoyl}-2-methylphenyl)-3-[3-(naphthalen-1-yloxy)propyl]pyrazolo[1,5-a]pyridine-2-carboxylic acid · ligand · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 2 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	62	0.47	0.84	14	empty
2	75	0.43	0.80	15	empty
3	80	0.35	0.75	16	empty
4	88	0.35	0.74	15	empty
5	51	0.31	0.75	11	empty

Interfaces

1 interface between chains.

A–B · 3508 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

3WIZ · Crystal structure of Bcl-xL in complex with compound 10 · 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 0.65

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 3WIZ · PDBe 3WIZ · UniProt Q07817

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.