MolNFT v1 · #104709 · protein
Crystal structure of aminopeptidase N in complex with the phosphinic dipeptide analogue ll-(R,S)-2-(pyridin-3-YL)ETHYLGLYP[CH2]PHE
4QIR: “Crystal structure of aminopeptidase N in complex with the phosphinic dipeptide analogue…”. X-ray diffraction, 3 ligands (379, ZN, SO4), 8 pockets (best druggability 0.77). MolNFT v1 #104709 on GenesisL1: 3D structure, binding sites…
- PDB
- 4QIR
- Type
- protein
- Length
- 864 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase N
- EC
- 3.4.11.2
- UniProt
- Q9JYV4
- Ligands
- 379, ZN, SO4
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopeptidase N (EC 3.4.11.2) | protein | 864 | 45% helix, 23% strand | Q9JYV4 |
Ligands and binding sites
- 379 · 3-{[(R)-1-amino-3-(pyridin-3-yl)propyl](hydroxy)phosphoryl}-(S)-2-benzylpropanoic acid · ligand · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 6 copies · chains A
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.77 | 0.87 | 53 | empty |
| 2 | 199 | 0.68 | 0.86 | 37 | 379, GOL |
| 3 | 449 | 0.63 | 0.77 | 48 | empty |
| 4 | 157 | 0.47 | 0.77 | 27 | empty |
| 5 | 55 | 0.47 | 0.85 | 14 | empty |
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4QIR · Crystal structure of Aminopeptidase N in complex with the phosphinic dipeptide analogue… · the same entry in another collection · 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 Q9JYV4
- Elsewhere: RCSB PDB 4QIR · PDBe 4QIR · UniProt Q9JYV4
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