Research workbench
Crystal structure of PDE4D complexed with a novel inhibitor
Analyse Crystal structure of PDE4D complexed with a novel inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IMT
- Type
- protein
- Length
- 644 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.483
- Source
- Homo sapiens
- Molecule
- cAMP-specific 3',5'-cyclic phosphodiesterase 4D
- EC
- 3.1.4.53
- UniProt
- Q08499
- Ligands
- AK0, ZN, MG
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · resolution 1.483 · 2 distinct chains · 67% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | cAMP-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 324 | 67% helix, 1% strand | Q08499 |
| B | cAMP-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 320 | 67% helix, 1% strand | Q08499 |
Ligands and binding sites
- AK0 · (1S)-1-[2-(6-fluoro-1H-indol-3-yl)ethyl]-6,7-dimethoxy-3,4-dihydroisoquinoline-2(1H)-carbaldehyde · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.72 | 0.82 | 45 | MG, EDO, AK0 |
| 2 | 418 | 0.71 | 0.82 | 41 | MG, EDO, AK0 |
| 3 | 212 | 0.57 | 0.79 | 24 | EDO |
| 4 | 218 | 0.56 | 0.79 | 25 | EDO |
| 5 | 115 | 0.39 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 793 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6IMT · Crystal structure of PDE4D complexed with a novel inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
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 6IMT · PDBe 6IMT · UniProt Q08499
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