Research workbench
Crystal structure of PDE5A1 catalytic domain in complex with vardenafil
Analyse Crystal structure of PDE5A1 catalytic domain in complex with vardenafil in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B2R
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-specific 3',5'-cyclic phosphodiesterase
- EC
- 3.1.4.35
- UniProt
- O76074
- Ligands
- VDN
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.35) | protein | 297 | 71% helix, 0% strand | O76074 |
| B | Cgmp-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.35) | protein | 287 | 67% helix, 0% strand | O76074 |
Ligands and binding sites
- VDN · 2-{2-ethoxy-5-[(4-ethylpiperazin-1-yl)sulfonyl]phenyl}-5-methyl-7-propylimidazo[5,1-f][1,2,4]triazin-4(1H)-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 789 | 0.75 | 0.80 | 75 | empty |
| 2 | 290 | 0.71 | 0.84 | 32 | VDN |
| 3 | 263 | 0.70 | 0.85 | 26 | VDN |
| 4 | 422 | 0.64 | 0.78 | 45 | empty |
| 5 | 120 | 0.55 | 0.83 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 792 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3B2R · Crystal Structure of PDE5A1 catalytic domain in complex with Vardenafil · 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 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 O76074
- Elsewhere: RCSB PDB 3B2R · PDBe 3B2R · UniProt O76074
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