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Crystal structure of BCL-xl in complex with inhibitor (wehi-539)

Analyse Crystal structure of BCL-xl in complex with inhibitor (wehi-539) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ZLR
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: X0B, SO4
Pockets: 3 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BCL-2-like protein 1	protein	146	77% helix, 0% strand	Q07817
B	BCL-2-like protein 1	protein	144	72% helix, 0% strand	Q07817

Ligands and binding sites

X0B · 5-[3-[4-(aminomethyl)phenoxy]propyl]-2-[(8E)-8-(1,3-benzothiazol-2-ylhydrazinylidene)-6,7-dihydro-5H-naphthalen-2-yl]-1,3-thiazole-4-carboxylic acid · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains A, B
EDO · 1,2-ethanediol · additive · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	263	0.61	0.80	36	empty
2	173	0.55	0.80	25	X0B
3	141	0.50	0.79	18	X0B

Interfaces

1 interface between chains.

A–B · 2155 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

3ZLR · Crystal structure of BCL-XL in complex with inhibitor (WEHI-539) · the same entry in another collection · chain A against A, 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 B against A, TM-score 0.74

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 3ZLR · PDBe 3ZLR · UniProt Q07817

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