MolNFT v1 · #23535 · protein
In situ extension as an approach for identifying novel alpha-amylase inhibitors
1U33 · Alpha-amylase, pancreatic: “In situ extension as an approach for identifying novel alpha-amylase inhibitors”. X-ray diffraction, 4 ligands (LM2, NAG, CA), 4 pockets (best druggability 0.56). MolNFT v1 #23535 on GenesisL1: 3D…
- PDB
- 1U33
- 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
- LM2, NAG, CA, CL
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-amylase, pancreatic (EC 3.2.1.1) | protein | 496 | 28% helix, 24% strand | P04746 |
Ligands and binding sites
- LM2 · 4'-O-methyl-maltosyl-alpha (1,4)-(Z, 3S,4S,5R,6R)-3,4,5-trihydroxy-6-hydroxymethyl-piperidin-2-one · 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.56 | 0.78 | 24 | LM2 |
| 2 | 77 | 0.37 | 0.77 | 18 | empty |
| 3 | 52 | 0.37 | 0.80 | 12 | empty |
| 4 | 86 | 0.34 | 0.75 | 20 | empty |
Modifications
Observed in the structure: 5 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 1U33 · 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 1U33 · PDBe 1U33 · UniProt P04746
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