MolNFT v1 · #91713 · protein
Human METAP1 with bengamide analog Y08, in mn form
4FLJ · Methionine aminopeptidase 1: “Human METAP1 with bengamide analog Y08, in mn form”. X-ray diffraction, 3 ligands (Y08, MN, NA), 1 pocket (best druggability 0.60). MolNFT v1 #91713 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4FLJ
- Type
- protein
- Length
- 304 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine aminopeptidase 1
- EC
- 3.4.11.18
- UniProt
- P53582
- Ligands
- Y08, MN, NA
- Pockets
- 1 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine aminopeptidase 1 (EC 3.4.11.18) | protein | 304 | 28% helix, 23% strand | P53582 |
Ligands and binding sites
- Y08 · (E,2R,3R,4S,5R)-N-[[(3S)-1-cyclopropylcarbonylpiperidin-3-yl]methyl]-2-methoxy-8,8-dimethyl-3,4,5-tris(oxidanyl)non-6-enamide · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.60 | 0.78 | 36 | Y08 |
Compared structures
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 P53582
- Elsewhere: RCSB PDB 4FLJ · PDBe 4FLJ · UniProt P53582
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