MolNFT v1 · #99680 · protein

BCL_2-navitoclax analog (with indole) complex

4MAN · Apoptosis regulator BCL-2: “BCL_2-navitoclax analog (with indole) complex”. X-ray diffraction, 1 ligand (1Y1), 6 pockets (best druggability 0.54). MolNFT v1 #99680 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4MAN
Type: protein
Length: 272 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apoptosis regulator BCL-2
UniProt: P10415
Ligands: 1Y1
Pockets: 6 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Apoptosis regulator BCL-2	protein	136	76% helix, 0% strand	P10415

Ligands and binding sites

1Y1 · 4-[4-({4'-chloro-3-[2-(dimethylamino)ethoxy]biphenyl-2-yl}methyl)piperazin-1-yl]-2-(1H-indol-5-yloxy)-N-({3-nitro-4-[(tetrahydro-2H-pyran-4-ylmethyl)amino]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

6 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	243	0.54	0.77	28	empty
2	113	0.49	0.80	15	empty
3	115	0.49	0.80	16	empty
4	60	0.38	0.80	14	empty
5	56	0.38	0.80	14	empty

Interfaces

1 interface between chains.

A–B · 245 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4MAN · Bcl_2-Navitoclax Analog (with Indole) 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 A against A, TM-score 0.96

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 4MAN · PDBe 4MAN · UniProt P10415

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