MolNFT v1 · #21872 · protein
Catalytic domain of human phosphodiesterase 3B in complex with a dihydropyridazine inhibitor
1SO2 · Cgmp-inhibited 3',5'-cyclic phosphodiesterase B: “Catalytic domain of human phosphodiesterase 3B in complex with a dihydropyridazine inhibitor”. X-ray diffraction, 3 ligands (HG9, 666, MG), 14 pockets (best druggability 0.79).…
- PDB
- 1SO2
- Type
- protein
- Length
- 1,463 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-inhibited 3',5'-cyclic phosphodiesterase B
- EC
- 3.1.4.17
- UniProt
- Q13370
- Ligands
- HG9, 666, MG
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 61% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cgmp-inhibited 3',5'-cyclic phosphodiesterase B (EC 3.1.4.17) | protein | 363 | 62% helix, 2% strand | Q13370 |
| C | Cgmp-inhibited 3',5'-cyclic phosphodiesterase B (EC 3.1.4.17) | protein | 372 | 61% helix, 2% strand | Q13370 |
| D | Cgmp-inhibited 3',5'-cyclic phosphodiesterase B (EC 3.1.4.17) | protein | 365 | 61% helix, 1% strand | Q13370 |
Ligands and binding sites
- HG9 · 1-deoxy-1-[(2-hydroxyethyl)(nonanoyl)amino]hexitol · ligand · 4 copies · chains A, B
- 666 · 6-(4-{[2-(3-iodobenzyl)-3-oxocyclohex-1-en-1-yl]amino}phenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-one · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.79 | 0.81 | 128 | MG, 666 |
| 2 | 988 | 0.76 | 0.78 | 109 | MG, 666 |
| 3 | 421 | 0.72 | 0.82 | 44 | MG, 666 |
| 4 | 862 | 0.71 | 0.76 | 95 | empty |
| 5 | 121 | 0.47 | 0.79 | 18 | empty |
Interfaces
5 interfaces between chains.
- C–D · 873 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 842 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 424 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 261 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 178 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1SO2 · CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 3B In COMPLEX WITH A DIHYDROPYRIDAZINE… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13370 · AlphaFold monomer V2.0 prediction for cgmp-inhibited 3',5'-cyclic phosphodiesterase B… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q13370
- Elsewhere: RCSB PDB 1SO2 · PDBe 1SO2 · UniProt Q13370
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