GL1X · GenesisL1 explorer

MolNFT v1 · #69201 · protein

Caspase 3 bound to a covalent inhibitor

3KJF · Caspase-3: “Caspase 3 bound to a covalent inhibitor”. X-ray diffraction, 1 ligand (B92), 1 pocket (best druggability 0.45). MolNFT v1 #69201 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
3KJF
Type
protein
Length
242 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Caspase-3
EC
3.4.22.56
UniProt
P42574
Ligands
B92
Pockets
1 · best druggability 0.45

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ACaspase-3 (EC 3.4.22.56)protein14027% helix, 31% strandP42574
BCaspase-3 (EC 3.4.22.56)protein10230% helix, 16% strandP42574

Ligands and binding sites

  • B92 · (3S)-3-({[(5S,10aS)-2-{(2S)-4-carboxy-2-[(phenylacetyl)amino]butyl}-1,3-dioxo-2,3,5,7,8,9,10,10a-octahydro-1H-[1,2,4]triazolo[1,2-a]cinnolin-5-yl]carbonyl}amino)-4-oxopentanoic acid · ligand · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11830.450.7426B92

Interfaces

1 interface between chains.

  • A–B · 2262 Ų buried · 37 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

  • 3KJF · Caspase 3 Bound to a covalent 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 1.00

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