MolNFT v1 · #23530 · protein
In situ extension as an approach for identifying novel alpha-amylase inhibitors, structure containing D-gluconhydroximo-1,5-lactam
1U2Y · Alpha-amylase, pancreatic: “In situ extension as an approach for identifying novel alpha-amylase inhibitors, structure containing…”. X-ray diffraction, 4 ligands (GOX, NAG, CA), 3 pockets (best druggability 0.57). MolNFT v1 #23530…
- PDB
- 1U2Y
- Type
- protein
- Length
- 496 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-amylase, pancreatic
- EC
- 3.2.1.1
- UniProt
- P04746
- Ligands
- GOX, NAG, CA, CL
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-amylase, pancreatic (EC 3.2.1.1) | protein | 496 | 29% helix, 24% strand | P04746 |
Ligands and binding sites
- GOX · (2S,3S,4R,5R)-6-(hydroxyamino)-2-(hydroxymethyl)-2,3,4,5-tetrahydropyridine-3,4,5-triol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- CA · Calcium ion · metal · 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 | 241 | 0.57 | 0.78 | 23 | GOX |
| 2 | 90 | 0.37 | 0.76 | 18 | empty |
| 3 | 83 | 0.34 | 0.75 | 18 | empty |
Modifications
Observed in the structure: 5 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 1U2Y · In situ extension as an approach for identifying novel alpha-amylase inhibitors… · the same entry in another collection · chain A against A, TM-score 1.00
- P04746 · AlphaFold monomer V2.0 prediction for pancreatic alpha-amylase (P04746) · 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 P04746
- Elsewhere: RCSB PDB 1U2Y · PDBe 1U2Y · UniProt P04746
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