Research workbench
Crystal structure of the catalytic domain of PDE4D2 with compound 10o
Analyse Crystal structure of the catalytic domain of PDE4D2 with compound 10o in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SL8
- Type
- protein
- Length
- 1,299 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Homo sapiens
- Molecule
- cAMP-specific 3',5'-cyclic phosphodiesterase 4D
- EC
- 3.1.4.17
- UniProt
- Q08499
- Ligands
- JN7, ZN, PO4
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.6 · 4 distinct chains · 67% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | cAMP-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 327 | 67% helix, 1% strand | Q08499 |
| B | cAMP-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 324 | 67% helix, 1% strand | Q08499 |
| C | cAMP-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 324 | 67% helix, 1% strand | Q08499 |
| D | cAMP-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 324 | 68% helix, 1% strand | Q08499 |
Ligands and binding sites
- JN7 · 3-cyclopentyl 6-ethenyl 2-[(thiophen-2-ylacetyl)amino]-4,7-dihydrothieno[2,3-c]pyridine-3,6(5H)-dicarboxylate · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains B, C
- EDO · 1,2-ethanediol · additive · 30 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, C, D
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.84 | 0.89 | 84 | empty |
| 2 | 426 | 0.82 | 0.90 | 68 | EDO |
| 3 | 1084 | 0.79 | 0.80 | 97 | EDO, PEG |
| 4 | 459 | 0.71 | 0.81 | 39 | ZN, JN7 |
| 5 | 430 | 0.71 | 0.81 | 50 | ZN, JN7 |
Interfaces
6 interfaces between chains.
- A–C · 948 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 876 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 799 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 703 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 229 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3SL8 · Crystal structure of the catalytic domain of PDE4D2 with compound 10O · the same entry in another collection · chain D against D, 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 D 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 3SL8 · PDBe 3SL8 · UniProt Q08499
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