MolNFT v1 · #123298 · protein
Potent, reversible METAP2 inhibitors via fragment based drug discovery
5JFR · Methionine aminopeptidase 2: “Potent, reversible METAP2 inhibitors via fragment based drug discovery”. X-ray diffraction, 2 ligands (6KP, MN), 5 pockets (best druggability 0.69). MolNFT v1 #123298 on GenesisL1: 3D structure, binding…
- PDB
- 5JFR
- Type
- protein
- Length
- 366 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine aminopeptidase 2
- EC
- 3.4.11.18
- UniProt
- P50579
- Ligands
- 6KP, MN
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine aminopeptidase 2 (EC 3.4.11.18) | protein | 366 | 32% helix, 26% strand | P50579 |
Ligands and binding sites
- 6KP · 7-fluoro-4-(5-methyl-3H-imidazo[4,5-b]pyridin-6-yl)-2,4-dihydropyrazolo[4,3-b]indole · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.69 | 0.84 | 38 | 6KP |
| 2 | 50 | 0.49 | 0.86 | 15 | empty |
| 3 | 63 | 0.33 | 0.76 | 17 | empty |
| 4 | 54 | 0.27 | 0.74 | 16 | empty |
| 5 | 56 | 0.27 | 0.73 | 13 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5JFR · Potent, Reversible MetAP2 Inhibitors via Fragment Based Drug Discovery · the same entry in another collection · chain A against A, TM-score 1.00
- P50579 · AlphaFold monomer V2.0 prediction for methionine aminopeptidase 2 (P50579) · 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 P50579
- Elsewhere: RCSB PDB 5JFR · PDBe 5JFR · UniProt P50579
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