MolNFT v1 · #67552 · protein

Crystal structure of BCL-xl in complex with W1191542

3INQ · BCL-2-like protein 1: “Crystal structure of BCL-xl in complex with W1191542”. X-ray diffraction, 2 ligands (X0J, CL), 5 pockets (best druggability 0.57). MolNFT v1 #67552 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3INQ
Type: protein
Length: 278 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BCL-2-like protein 1
UniProt: Q07817
Ligands: X0J, CL
Pockets: 5 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BCL-2-like protein 1	protein	138	78% helix, 0% strand	Q07817
B	BCL-2-like protein 1	protein	140	79% helix, 0% strand	Q07817

Ligands and binding sites

X0J · 4-[4-(biphenyl-3-ylmethyl)piperazin-1-yl]-N-{[4-({(1R)-3-(dimethylamino)-1-[(phenylsulfanyl)methyl]propyl}amino)-3-nitrophenyl]sulfonyl}benzamide · ligand · 2 copies · chains A, B
CL · Chloride ion · ion · chains B
EDO · 1,2-ethanediol · additive · 11 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	211	0.57	0.80	35	EDO
2	88	0.39	0.76	15	empty
3	64	0.31	0.74	10	empty
4	58	0.29	0.74	16	empty
5	51	0.27	0.74	11	empty

Interfaces

1 interface between chains.

A–B · 2194 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

3INQ · Crystal structure of BCL-XL in complex with W1191542 · 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 3INQ · PDBe 3INQ · UniProt Q07817

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