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Endothiapepsin in complex with an inhibitor based on the gewald reaction

Analyse Endothiapepsin in complex with an inhibitor based on the gewald reaction in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3PSY
Type
protein
Length
330 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Endothiapepsin
EC
3.4.23.22
UniProt
P11838
Ligands
RB9
Pockets
1 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 12% helix, 45% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AEndothiapepsin (EC 3.4.23.22)protein33012% helix, 45% strandP11838

Ligands and binding sites

  • RB9 · N-benzyl-2-({N-[2-(1H-indol-3-yl)ethyl]glycyl}amino)-4-phenylthiophene-3-carboxamide · ligand · chains A
  • DMS · Dimethyl sulfoxide · additive · chains A
  • GOL · Glycerol · additive · chains A
  • PG4 · Tetraethylene glycol · additive · chains A
  • 1PE · Pentaethylene glycol · additive · chains A

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13280.570.7535RB9, DMS, PG4, 1PE

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

  • 3PSY · Endothiapepsin in complex with an inhibitor based on the Gewald reaction · the same entry in another collection · chain A against A, TM-score 1.00
  • P11838 · AlphaFold monomer V2.0 prediction for endothiapepsin (P11838) · a predicted model of the same protein · chain A against A, TM-score 1.00

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