Research workbench
Phosphonic arginine mimetics as inhibitors of the M17 aminopeptidases from plasmodium falciparum
Analyse Phosphonic arginine mimetics as inhibitors of the M17 aminopeptidases from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K3N
- Type
- protein
- Length
- 6,178 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M17 leucyl aminopeptidase
- UniProt
- Q8IL11
- Ligands
- 1OT, ZN, SO4, CO3
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 9 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | M17 leucyl aminopeptidase | protein | 519 | 35% helix, 22% strand | Q8IL11 |
| B, C, I | M17 leucyl aminopeptidase | protein | 518 | 36% helix, 22% strand | Q8IL11 |
| D | M17 leucyl aminopeptidase | protein | 514 | 36% helix, 22% strand | Q8IL11 |
| E | M17 leucyl aminopeptidase | protein | 510 | 35% helix, 22% strand | Q8IL11 |
| F | M17 leucyl aminopeptidase | protein | 511 | 35% helix, 22% strand | Q8IL11 |
| H | M17 leucyl aminopeptidase | protein | 516 | 36% helix, 22% strand | Q8IL11 |
| J | M17 leucyl aminopeptidase | protein | 513 | 36% helix, 22% strand | Q8IL11 |
| K | M17 leucyl aminopeptidase | protein | 509 | 35% helix, 23% strand | Q8IL11 |
| L | M17 leucyl aminopeptidase | protein | 513 | 36% helix, 22% strand | Q8IL11 |
Ligands and binding sites
- 1OT · {(R)-amino[4-(1H-pyrazol-1-yl)phenyl]methyl}phosphonic acid · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- ZN · Zinc ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 21 copies · chains A, B, C, D, E, F, G, J, H, I, K, L
- CO3 · Carbonate ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- 1PE · Pentaethylene glycol · additive · 34 copies · chains A, C, D, E, F, G, I, J, K, L
- 2PE · Nonaethylene glycol · additive · 12 copies · chains B, C, D, E, F, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.77 | 0.81 | 64 | empty |
| 2 | 1008 | 0.76 | 0.79 | 93 | CO3, 1OT |
| 3 | 686 | 0.76 | 0.81 | 108 | 1PE |
| 4 | 1042 | 0.74 | 0.77 | 107 | empty |
| 5 | 852 | 0.74 | 0.78 | 67 | 1OT |
Interfaces
26 interfaces between chains.
- H–I · 1511 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1504 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1503 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 1499 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1492 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 4K3N · Phosphonic Arginine Mimetics as Inhibitors of the M17 Aminopeptidases from Plasmodium… · 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 Q8IL11
- Elsewhere: RCSB PDB 4K3N · PDBe 4K3N · UniProt Q8IL11
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