Research workbench
The crystal structure of inhibitor-15 covalently bound to PDE6D
Analyse The crystal structure of inhibitor-15 covalently bound to PDE6D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NAL
- Type
- protein
- Length
- 150 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
- 8RQ
- Pockets
- 1 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase subunit delta | protein | 150 | 14% helix, 58% strand | O43924 |
Ligands and binding sites
- 8RQ · ~{N}4-[(4-chlorophenyl)methyl]-~{N}1-(cyclohexylmethyl)-~{N}4-cyclopentyl-~{N}1-[(~{Z})-4-[(~{E})-methyliminomethyl]-5-oxidanyl-hex-4-enyl]benzene-1,4-disulfonamide · ligand · chains B
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 | 372 | 0.83 | 0.91 | 41 | 8RQ |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5NAL · The crystal structure of inhibitor-15 covalently bound to PDE6D · 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 0.97
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 5NAL · PDBe 5NAL · UniProt O43924
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