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MolNFT v1 · #37130 · protein

Human cathepsin S with cra-27934, a nitrile inhibitor

2FRA: “Human cathepsin S with cra-27934, a nitrile inhibitor”. X-ray diffraction, 1 ligand (CRV), 1 pocket (best druggability 0.72). MolNFT v1 #37130 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
2FRA
Type
protein
Length
435 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
CRV
Pockets
1 · best druggability 0.72

Structure

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

ChainMoleculeTypeResiduesSecondary structureUniProt
ACathepsin S (EC 3.4.22.27)protein21729% helix, 24% strandP25774
BCathepsin S (EC 3.4.22.27)protein21829% helix, 24% strandP25774

Ligands and binding sites

  • CRV · N-[1-(aminomethyl)cyclopropyl]-3-(benzylsulfonyl)-N~2~-[(1S)-2,2,2-trifluoro-1-(4-hydroxyphenyl)ethyl]-L-alaninamide · ligand · 2 copies · 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, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
15270.720.8168CRV

Interfaces

1 interface between chains.

  • A–B · 753 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

  • 2FRA · Human Cathepsin S with CRA-27934, a Nitrile Inhibitor · 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 A against A, TM-score 1.00

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