Research workbench

Caspase-3 tethered to irreversible inhibitor

Analyse Caspase-3 tethered to irreversible inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1NMS
Type: protein
Length: 480 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-3
EC: 3.4.22.-
UniProt: P42574
Ligands: 161
Pockets: 6 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Caspase-3 (EC 3.4.22.-)	protein	240	29% helix, 26% strand	P42574

Ligands and binding sites

161 · 5-[4-(1-carboxymethyl-2-oxo-propylcarbamoyl)-benzylsulfamoyl]-2-hydroxy-benzoic acid · 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	321	0.66	0.81	43	empty
2	122	0.40	0.75	30	161
3	68	0.35	0.77	15	161
4	62	0.35	0.77	19	empty
5	72	0.34	0.75	19	empty

Interfaces

1 interface between chains.

A–B · 2545 Å² buried · 44 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

1NMS · Caspase-3 tethered to irreversible inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
P42574 · AlphaFold monomer V2.0 prediction for caspase-3 (P42574) · 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 P42574
Elsewhere: RCSB PDB 1NMS · PDBe 1NMS · UniProt P42574

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