GL1X · GenesisL1 explorer

MolNFT v1 · #39045 · protein

Cathepsin S in complex with non covalent arylaminoethyl amide.

2HHN: “Cathepsin S in complex with non covalent arylaminoethyl amide.”. X-ray diffraction, 2 ligands (GNQ, SO4), 2 pockets (best druggability 0.69). MolNFT v1 #39045 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
2HHN
Type
protein
Length
437 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Cathepsin S
EC
3.4.22.27
UniProt
P25774
Ligands
GNQ, SO4
Pockets
2 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 23% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ACathepsin S (EC 3.4.22.27)protein22029% helix, 24% strandP25774
BCathepsin S (EC 3.4.22.27)protein21730% helix, 23% strandP25774

Ligands and binding sites

  • GNQ · N-[(1R)-1-[(benzylsulfonyl)methyl]-2-{[(1S)-1-methyl-2-{[4-(trifluoromethoxy)phenyl]amino}ethyl]amino}-2-oxoethyl]morpholine-4-carboxamide · ligand · chains B
  • SO4 · Sulfate ion · ion · 4 copies · chains A

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

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
14610.690.8051GNQ
2780.310.7324empty

Interfaces

1 interface between chains.

  • A–B · 760 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

  • 2HHN · Cathepsin S in complex with non covalent arylaminoethyl amide. · the same entry in another collection · chain A against A, TM-score 1.00
  • P25774 · AlphaFold monomer V2.0 prediction for cathepsin S (P25774) · a predicted model of the same protein · chain B against A, TM-score 0.99

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