MolNFT v1 · #23885 · protein
Crystal structure of human phosphodiesterase 5 complexed with TADALAFIL(CIALIS)
1UDU · Cgmp-specific 3',5'-cyclic phosphodiesterase: “Crystal structure of human phosphodiesterase 5 complexed with TADALAFIL(CIALIS)”. X-ray diffraction, 3 ligands (CIA, ZN, MG), 7 pockets (best druggability 0.80). MolNFT v1 #23885 on…
- PDB
- 1UDU
- Type
- protein
- Length
- 626 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-specific 3',5'-cyclic phosphodiesterase
- EC
- 3.1.4.17
- UniProt
- O76074
- Ligands
- CIA, ZN, MG
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cgmp-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 313 | 58% 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 · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 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 | 531 | 0.80 | 0.86 | 49 | MG, CIA |
| 2 | 525 | 0.79 | 0.86 | 52 | MG, CIA |
| 3 | 412 | 0.68 | 0.80 | 46 | empty |
| 4 | 425 | 0.67 | 0.79 | 43 | empty |
| 5 | 122 | 0.59 | 0.85 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 759 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1UDU · Crystal structure of Human Phosphodiesterase 5 complexed with tadalafil(Cialis) · 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 1UDU · PDBe 1UDU · UniProt O76074
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