MolNFT v1 · #161434 · protein
Crystal structure of human methionine aminopeptidase-2 in complex with an inhibitor 2-oxo-1-phenyl-pyrrolidine-3-carboxylic acid (2- thiophen-2-yl-ethyl)-amide
6QEG · Methionine aminopeptidase 2: “Crystal structure of human methionine aminopeptidase-2 in complex with an inhibitor…”. X-ray diffraction, 2 ligands (K4K, MN), 4 pockets (best druggability 0.68). MolNFT v1 #161434 on GenesisL1: 3D…
- PDB
- 6QEG
- Type
- protein
- Length
- 364 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
- K4K, MN
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine aminopeptidase 2 (EC 3.4.11.18) | protein | 364 | 33% helix, 26% strand | P50579 |
Ligands and binding sites
- K4K · (3~{S})-3-oxidanyl-2-oxidanylidene-1-phenyl-~{N}-(2-thiophen-2-ylethyl)pyrrolidine-3-carboxamide · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.68 | 0.85 | 45 | K4K |
| 2 | 59 | 0.47 | 0.84 | 16 | empty |
| 3 | 59 | 0.33 | 0.77 | 16 | empty |
| 4 | 64 | 0.31 | 0.75 | 15 | GOL |
Compared structures
- 6QEG · CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR… · 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 6QEG · PDBe 6QEG · UniProt P50579
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