Research workbench
Crystal structure of rat neurolysin with bound pyrazolidin inhibitor
Analyse Crystal structure of rat neurolysin with bound pyrazolidin inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FXY
- Type
- protein
- Length
- 1,328 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neurolysin, mitochondrial
- EC
- 3.4.24.16
- UniProt
- P42676
- Ligands
- 0W2, ZN
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P, Q | Neurolysin, mitochondrial (EC 3.4.24.16) | protein | 664 | 55% helix, 7% strand | P42676 |
Ligands and binding sites
- 0W2 · 1-{(2S)-1-[(3R)-3-(2-chlorophenyl)-2-(2-fluorophenyl)pyrazolidin-1-yl]-1-oxopropan-2-yl}-3-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]urea · ligand · 2 copies · chains P, Q
- ZN · Zinc ion · metal · 2 copies · chains P, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.77 | 0.79 | 85 | 0W2 |
| 2 | 825 | 0.76 | 0.80 | 69 | 0W2 |
| 3 | 595 | 0.71 | 0.79 | 51 | empty |
| 4 | 585 | 0.70 | 0.79 | 50 | empty |
| 5 | 262 | 0.69 | 0.84 | 38 | empty |
Compared structures
- 4FXY · Crystal structure of rat neurolysin with bound pyrazolidin inhibitor · the same entry in another collection · chain P against P, TM-score 1.00
- P42676 · AlphaFold monomer V2.0 prediction for neurolysin, mitochondrial (P42676) · a predicted model of the same protein · chain P against A, TM-score 0.97
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 P42676
- Elsewhere: RCSB PDB 4FXY · PDBe 4FXY · UniProt P42676
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