MolNFT v1 · #75006 · protein
Discovery of novel cyanamide-based inhibitors of cathepsin C
3PDF · Dipeptidyl peptidase 1: “Discovery of novel cyanamide-based inhibitors of cathepsin C”. X-ray diffraction, 3 ligands (LXV, NAG, CL), 3 pockets (best druggability 0.53). MolNFT v1 #75006 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3PDF
- Type
- protein
- Length
- 351 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 1
- EC
- 3.4.14.1
- UniProt
- P53634
- Ligands
- LXV, NAG, CL
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 1 (EC 3.4.14.1) | protein | 351 | 19% helix, 36% strand | P53634 |
Ligands and binding sites
- LXV · 2,5-dibromo-N-{(3R,5S)-1-[(Z)-iminomethyl]-5-methylpyrrolidin-3-yl}benzenesulfonamide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.53 | 0.82 | 27 | LXV, CL |
| 2 | 93 | 0.41 | 0.77 | 19 | empty |
| 3 | 63 | 0.34 | 0.77 | 17 | empty |
Modifications
Observed in the structure: 5 disulfide, 3 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P53634
- Elsewhere: RCSB PDB 3PDF · PDBe 3PDF · UniProt P53634
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