Research workbench
Catalytic domain of human phosphodiesterase 5A in complex with tadalafil
Analyse Catalytic domain of human phosphodiesterase 5A in complex with tadalafil in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XOZ
- Type
- protein
- Length
- 326 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-specific 3',5'-cyclic phosphodiesterase
- EC
- 3.1.4.17
- UniProt
- O76074
- Ligands
- CIA, ZN, MG
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 326 | 72% helix, 0% strand | O76074 |
Ligands and binding sites
- CIA · 6-benzo[1,3]dioxol-5-yl-2-methyl-2,3,6,7,12,12A-hexahydro-pyrazino[1',2':1,6]pyrido[3,4-b]indole-1,4-dione · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.73 | 0.82 | 46 | MG, CIA |
| 2 | 62 | 0.55 | 0.89 | 23 | empty |
| 3 | 100 | 0.38 | 0.75 | 16 | empty |
Compared structures
- 1XOZ · Catalytic Domain Of Human Phosphodiesterase 5A In Complex With Tadalafil · the same entry in another collection · chain A against A, TM-score 1.00
- O76074 · AlphaFold monomer V2.0 prediction for cgmp-specific 3',5'-cyclic phosphodiesterase… · a predicted model of the same protein · chain A 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 O76074
- Elsewhere: RCSB PDB 1XOZ · PDBe 1XOZ · UniProt O76074
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