Research workbench

BCL_2-navitoclax (abt-263) complex

Analyse BCL_2-navitoclax (abt-263) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LVT
Type: protein
Length: 278 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apoptosis regulator BCL-2
UniProt: P10415
Ligands: 1XJ
Pockets: 4 · best druggability 0.45

Structure

x-ray diffraction · 1 distinct chain · 74% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Apoptosis regulator BCL-2	protein	139	74% helix, 0% strand	P10415

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 · 2 copies · chains A, B

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

Pockets

4 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	105	0.45	0.78	15	empty
2	90	0.44	0.79	12	empty
3	60	0.38	0.79	20	empty
4	58	0.29	0.74	11	empty

Interfaces

1 interface between chains.

A–B · 351 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4LVT · Bcl_2-Navitoclax (ABT-263) Complex · the same entry in another collection · chain A against A, TM-score 1.00
P10415 · AlphaFold monomer V2.0 prediction for apoptosis regulator BCL-2 (P10415) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P10415
Elsewhere: RCSB PDB 4LVT · PDBe 4LVT · UniProt P10415

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