MolNFT v2 · #19111 · protein
Three dimensional structures of PDE4D in complex with roliprams and implication on inhibitor selectivity
1Q9M · cAMP-specific phosphodiesterase PDE4D2: “Three dimensional structures of PDE4D in complex with roliprams and implication on inhibitor selectivity”. X-ray diffraction at 2.3, 2 ligands (ROL, ZN), 14 pockets (best druggability 0.88).…
- PDB
- 1Q9M
- Type
- protein
- Length
- 1,324 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Homo sapiens
- Molecule
- cAMP-specific phosphodiesterase PDE4D2
- EC
- 3.1.4.17
- UniProt
- Q08499
- Ligands
- ROL, ZN
- Pockets
- 14 · best druggability 0.88
Structure
x-ray diffraction · resolution 2.3 · 3 distinct chains · 65% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | cAMP-specific phosphodiesterase PDE4D2 (EC 3.1.4.17) | protein | 334 | 65% helix, 1% strand | Q08499 |
| B | cAMP-specific phosphodiesterase PDE4D2 (EC 3.1.4.17) | protein | 327 | 66% helix, 1% strand | Q08499 |
| C | cAMP-specific phosphodiesterase PDE4D2 (EC 3.1.4.17) | protein | 329 | 65% helix, 0% strand | Q08499 |
Ligands and binding sites
- ROL · Rolipram · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1157 | 0.88 | 0.90 | 154 | empty |
| 2 | 471 | 0.73 | 0.82 | 40 | ZN, ROL |
| 3 | 412 | 0.73 | 0.83 | 39 | ZN, ROL |
| 4 | 473 | 0.72 | 0.82 | 46 | ZN, ROL |
| 5 | 189 | 0.72 | 0.89 | 36 | empty |
Interfaces
6 interfaces between chains.
- B–D · 990 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 933 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 857 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 808 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 242 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1Q9M · Three dimensional structures of PDE4D in complex with roliprams and implication on… · the same entry in another collection · chain A against A, TM-score 1.00
- Q08499 · AlphaFold monomer V2.0 prediction for camp-specific 3',5'-cyclic phosphodiesterase 4D… · a predicted model of the same protein · chain B 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 Q08499
- Elsewhere: RCSB PDB 1Q9M · PDBe 1Q9M · UniProt Q08499
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