Research workbench
Crystal structure of PDE5A1 in complex with icarisid II
Analyse Crystal structure of PDE5A1 in complex with icarisid II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H44
- 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
- 3.1.4.35
- UniProt
- O76074
- Ligands
- 7CA, ZN, MG
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.35) | protein | 326 | 66% helix, 2% strand | O76074 |
Ligands and binding sites
- 7CA · 5,7-dihydroxy-2-(4-methoxyphenyl)-8-(3-methylbutyl)-4-oxo-4H-chromen-3-yl 6-deoxy-alpha-L-mannopyranoside · 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 | 451 | 0.82 | 0.89 | 54 | MG, 7CA |
| 2 | 103 | 0.53 | 0.83 | 30 | empty |
| 3 | 85 | 0.39 | 0.77 | 21 | empty |
Compared structures
- 2H44 · Crystal structure of PDE5A1 in complex with icarisid II · 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 0.94
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 2H44 · PDBe 2H44 · UniProt O76074
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