MolNFT v1 · #111281 · protein
Crystal structure of porcine pancreatic elastase (ppe) in complex with the novel inhibitor JM102
4YM9 · Chymotrypsin-like elastase family member 1: “Crystal structure of porcine pancreatic elastase (ppe) in complex with the novel inhibitor JM102”. X-ray diffraction, 3 ligands (4E4, NA, SO4), 2 pockets (best druggability 0.60). MolNFT…
- PDB
- 4YM9
- Type
- protein
- Length
- 240 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chymotrypsin-like elastase family member 1
- EC
- 3.4.21.36
- UniProt
- P00772
- Ligands
- 4E4, NA, SO4
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chymotrypsin-like elastase family member 1 (EC 3.4.21.36) | protein | 240 | 11% helix, 38% strand | P00772 |
Ligands and binding sites
- 4E4 · 2-ethyl-2-(hydroxymethyl)-N-(6-methylpyridin-3-yl)butanamide · ligand · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- ACT · Acetate ion · additive · 5 copies · chains A
- GOL · Glycerol · additive · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.60 | 0.91 | 18 | empty |
| 2 | 67 | 0.32 | 0.76 | 20 | 4E4, SO4 |
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 4YM9 · Crystal structure of Porcine Pancreatic Elastase (PPE) in complex with the novel… · the same entry in another collection · chain A against A, TM-score 1.00
- P00772 · AlphaFold monomer V2.0 prediction for chymotrypsin-like elastase family member 1 (P00772) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P00772
- Elsewhere: RCSB PDB 4YM9 · PDBe 4YM9 · UniProt P00772
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