MolNFT v1 · #111996 · protein
Novel inhibitors of bacterial methionine aminopeptidase with broad- spectrum biochemical activity
4Z7M: “Novel inhibitors of bacterial methionine aminopeptidase with broad- spectrum biochemical activity”. X-ray diffraction, 2 ligands (4L9, MN), 5 pockets (best druggability 0.66). MolNFT v1 #111996 on GenesisL1: 3D structure, binding…
- PDB
- 4Z7M
- Type
- protein
- Length
- 522 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine aminopeptidase
- EC
- 3.4.11.18
- UniProt
- P0AE20
- Ligands
- 4L9, MN
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Methionine aminopeptidase (EC 3.4.11.18) | protein | 261 | 29% helix, 28% strand | P0AE20 |
Ligands and binding sites
- 4L9 · N~2~-[(3,5-difluorophenyl)acetyl]-N-[(3S,7R)-1-methyl-2-oxo-7-phenyl-2,3,4,7-tetrahydro-1H-azepin-3-yl]-L-alaninamide · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.66 | 0.77 | 56 | empty |
| 2 | 141 | 0.62 | 0.85 | 28 | 4L9 |
| 3 | 148 | 0.58 | 0.83 | 28 | 4L9 |
| 4 | 60 | 0.32 | 0.75 | 12 | empty |
| 5 | 56 | 0.29 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 392 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4Z7M · Novel Inhibitors of Bacterial Methionine Aminopeptidase with Broad-Spectrum Biochemical… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AE20 · AlphaFold monomer V2.0 prediction for methionine aminopeptidase (P0AE20) · 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 P0AE20
- Elsewhere: RCSB PDB 4Z7M · PDBe 4Z7M · UniProt P0AE20
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