MolNFT v1 · #117432 · protein
The crystal structure of pded in complex with inhibitor-2A
5E80 · Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic…: “The crystal structure of pded in complex with inhibitor-2A”. X-ray diffraction, 1 ligand (5KP), 2 pockets (best druggability 0.85). MolNFT v1 #117432 on GenesisL1: 3D structure…
- PDB
- 5E80
- Type
- protein
- Length
- 298 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase subunit delta
- UniProt
- O43924
- Ligands
- 5KP
- Pockets
- 2 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase subunit delta | protein | 149 | 16% helix, 57% strand | O43924 |
Ligands and binding sites
- 5KP · N-(3-chloro-2-methylphenyl)-4-(3,4-dimethyl-7-oxo-2-phenyl-2,7-dihydro-6H-pyrazolo[3,4-d]pyridazin-6-yl)butanamide · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.85 | 0.94 | 43 | 5KP |
| 2 | 637 | 0.82 | 0.86 | 66 | 5KP |
Interfaces
1 interface between chains.
- B–A · 339 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5E80 · The crystal structure of PDEd in complex with inhibitor-2a · the same entry in another collection · chain B against B, TM-score 1.00
- O43924 · AlphaFold monomer V2.0 prediction for retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O43924
- Elsewhere: RCSB PDB 5E80 · PDBe 5E80 · UniProt O43924
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.