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Tailoring small molecules for an allosteric site on procaspase-6

Analyse Tailoring small molecules for an allosteric site on procaspase-6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4NBN
Type: protein
Length: 499 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-6
EC: 3.4.22.59
UniProt: P55212
Ligands: 2J7, PO4
Pockets: 3 · best druggability 0.49

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-6 (EC 3.4.22.59)	protein	257	29% helix, 25% strand	P55212
B	Caspase-6 (EC 3.4.22.59)	protein	242	28% helix, 26% strand	P55212

Ligands and binding sites

2J7 · 2,2'-[pyrimidine-4,6-diylbis(iminomethanediyl)]diphenol · ligand · chains A, B
PO4 · Phosphate ion · ion · 9 copies · chains A, B

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

Pockets

3 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	138	0.49	0.79	25	2J7
2	87	0.36	0.75	19	PO4
3	66	0.33	0.76	19	PO4

Interfaces

1 interface between chains.

A–B · 1638 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

4NBN · Tailoring Small Molecules for an Allosteric Site on Procaspase-6 · the same entry in another collection · chain A against A, TM-score 1.00
P55212 · AlphaFold monomer V2.0 prediction for caspase-6 (P55212) · a predicted model of the same protein · chain B against A, TM-score 0.95

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 P55212
Elsewhere: RCSB PDB 4NBN · PDBe 4NBN · UniProt P55212

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