MolNFT v1 · #139169 · protein
The crystal structure pde delta in complex with (rac)-P9
5X72 · Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic…: “The crystal structure pde delta in complex with (rac)-P9”. X-ray diffraction, 2 ligands (P59, P69), 1 pocket (best druggability 0.87). MolNFT v1 #139169 on GenesisL1: 3D…
- PDB
- 5X72
- Type
- protein
- Length
- 149 residues
- Chains
- 1
- 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
- P59, P69
- Pockets
- 1 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase subunit delta | protein | 149 | 13% helix, 58% strand | O43924 |
Ligands and binding sites
- P59 · (2R)-2-(2-fluorophenyl)-3-phenyl-1,2-dihydroquinazolin-4-one · ligand · chains A
- P69 · (2S)-2-(2-fluorophenyl)-3-phenyl-1,2-dihydroquinazolin-4-one · ligand · 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 | 402 | 0.87 | 0.95 | 44 | P59, P69 |
Compared structures
- 5X72 · The crystal Structure PDE delta in complex with (rac)-p9 · the same entry in another collection · chain A against A, 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 A 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 O43924
- Elsewhere: RCSB PDB 5X72 · PDBe 5X72 · UniProt O43924
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