Research workbench

Crystal structure of BCL-xl bound to compound 7: (R)-3-(benzylthio)-2- (3-(4-chloro-[1,1':2',1'':3'',1'''-quaterphenyl]-4'''-carbonyl)-3-(4- METHYLBENZYL)UREIDO)PROPANOIC acid

Analyse Crystal structure of BCL-xl bound to compound 7: (R)-3-(benzylthio)-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6UVE
Type: protein
Length: 415 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BCL-2-like protein 1
UniProt: Q07817
Ligands: QHV
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 73% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BCL-2-like protein 1	protein	133	77% helix, 0% strand	Q07817
B	BCL-2-like protein 1	protein	134	75% helix, 1% strand	Q07817
C	BCL-2-like protein 1	protein	148	68% helix, 1% strand	Q07817

Ligands and binding sites

QHV · (R)-3-(benzylthio)-2-(3-(4-chloro-[1,1':2',1'':3'', 1'''-quaterphenyl]-4'''-carbonyl)-3-(4-methylbenzyl) ureido)propanoic acid · ligand · 3 copies · chains A, B, C
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1012	0.77	0.79	91	QHV
2	246	0.59	0.80	44	empty
3	97	0.49	0.81	24	empty
4	93	0.38	0.75	16	empty
5	76	0.35	0.76	19	empty

Interfaces

3 interfaces between chains.

A–B · 2131 Å² buried · 28 hydrogen bonds · protein-protein
A–C · 596 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 511 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6UVE · Crystal structure of BCL-XL bound to compound 7… · 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 0.78

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 6UVE · PDBe 6UVE · UniProt Q07817

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