Research workbench
Three dimensional structures of PDE4D in complex with roliprams and implication on inhibitor selectivity
Analyse Three dimensional structures of PDE4D in complex with roliprams and implication… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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