MolNFT v1 · #109442 · protein
X-ray crystal structure of the orally available aminopeptidase inhibitor, tosedostat, bound to the M1 alanyl aminopeptidase from P. falciparum
4X2U · M1 family aminopeptidase: “X-ray crystal structure of the orally available aminopeptidase inhibitor, tosedostat, bound to the M1 alanyl…”. X-ray diffraction, 3 ligands (TOD, MG, ZN), 11 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 4X2U
- Type
- protein
- Length
- 889 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M1 family aminopeptidase
- EC
- 3.4.11.-
- UniProt
- O96935
- Ligands
- TOD, MG, ZN
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M1 family aminopeptidase (EC 3.4.11.-) | protein | 889 | 45% helix, 21% strand | O96935 |
Ligands and binding sites
- TOD · (2S)-({(2R)-2-[(1S)-1-hydroxy-2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}amino)(phenyl)ethanoic acid · ligand · chains A
- MG · Magnesium ion · metal · 4 copies · chains A
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.79 | 0.87 | 69 | TOD, GOL |
| 2 | 362 | 0.77 | 0.87 | 51 | GOL |
| 3 | 663 | 0.69 | 0.77 | 65 | empty |
| 4 | 214 | 0.69 | 0.86 | 37 | empty |
| 5 | 330 | 0.58 | 0.76 | 46 | GOL, MG |
Compared structures
- 4X2U · X-ray crystal structure of the orally available aminopeptidase inhibitor, Tosedostat… · the same entry in another collection · chain A against A, TM-score 1.00
- O96935 · AlphaFold monomer V2.0 prediction for M1 family aminopeptidase (O96935) · 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 O96935
- Elsewhere: RCSB PDB 4X2U · PDBe 4X2U · UniProt O96935
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