Research workbench
Catalytic domain of human phosphodiesterase 5A in complex with sildenafil
Analyse Catalytic domain of human phosphodiesterase 5A in complex with sildenafil in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TBF
- 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
- VIA, ZN, MG
- Pockets
- 4 · 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
- VIA · 5-{2-ethoxy-5-[(4-methylpiperazin-1-yl)sulfonyl]phenyl}-1-methyl-3-propyl-1H,6H,7H-pyrazolo[4,3-d]pyrimidin-7-one · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.73 | 0.83 | 48 | MG, VIA |
| 2 | 59 | 0.55 | 0.88 | 20 | empty |
| 3 | 78 | 0.40 | 0.78 | 25 | empty |
| 4 | 98 | 0.36 | 0.74 | 17 | empty |
Compared structures
- 1TBF · Catalytic Domain Of Human Phosphodiesterase 5A in Complex with Sildenafil · 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 1TBF · PDBe 1TBF · UniProt O76074
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