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MolNFT v1 · #131697 · protein

Crystal structure of human cathepsin-S with bound ligand

5QC6 · Cathepsin S: “Crystal structure of human cathepsin-S with bound ligand”. X-ray diffraction, 1 ligand (BCJ), 2 pockets (best druggability 0.44). MolNFT v1 #131697 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
5QC6
Type
protein
Length
442 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
BCJ
Pockets
2 · best druggability 0.44

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 23% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BCathepsin S (EC 3.4.22.27)protein22130% helix, 23% strandP25774

Ligands and binding sites

  • BCJ · (4~{S})-1-[1-[(2~{S})-3-[3-[3-[2-(4-methylpiperidin-1-yl)ethylsulfanyl]-4-(trifluoromethyl)phenyl]-5-methylsulfonyl-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-1-yl]-2-oxidanyl-propyl]piperidin-4-yl]-4-oxidanyl-pyrrolidin-2-one · ligand · 2 copies · chains A, B

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11370.440.7627empty
21460.430.7527empty

Interfaces

1 interface between chains.

  • A–B · 17 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

  • 5QC6 · Crystal structure of human Cathepsin-S with bound ligand · 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 0.98

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