MolNFT v1 · #58964 · protein
Crystal structure of the PDE5A catalytic domain in complex with a novel inhibitor
3BJC · Cgmp-specific 3',5'-cyclic phosphodiesterase: “Crystal structure of the PDE5A catalytic domain in complex with a novel inhibitor”. X-ray diffraction, 3 ligands (WAN, ZN, MG), 2 pockets (best druggability 0.68). MolNFT v1 #58964 on…
- PDB
- 3BJC
- Type
- protein
- Length
- 311 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
- WAN, ZN, MG
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.35) | protein | 311 | 68% helix, 0% strand | O76074 |
Ligands and binding sites
- WAN · 5-ethoxy-4-(1-methyl-7-oxo-3-propyl-6,7-dihydro-1H-pyrazolo[4,3-d]pyrimidin-5-yl)thiophene-2-sulfonamide · 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
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.68 | 0.81 | 35 | MG, WAN |
| 2 | 105 | 0.51 | 0.82 | 27 | empty |
Compared structures
- 3BJC · Crystal structure of the PDE5A catalytic domain in complex with a novel inhibitor · 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 0.96
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 3BJC · PDBe 3BJC · UniProt O76074
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