MolNFT v2 · #223959 · protein
Crystal structure of PDE4D complexed with 7b-1
8WDN · cAMP-specific 3',5'-cyclic phosphodiesterase 4D: “Crystal structure of PDE4D complexed with 7b-1”. X-ray diffraction at 1.55, 3 ligands (W8E, MG, ZN), 5 pockets (best druggability 0.72). MolNFT v2 #223959 on GenesisL1: 3D structure…
- PDB
- 8WDN
- Type
- protein
- Length
- 648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.55
- Source
- Homo sapiens
- Molecule
- cAMP-specific 3',5'-cyclic phosphodiesterase 4D
- EC
- 3.1.4.53
- UniProt
- Q08499
- Ligands
- W8E, MG, ZN
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · resolution 1.55 · 1 distinct chain · 68% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | cAMP-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 324 | 68% helix, 1% strand | Q08499 |
Ligands and binding sites
- W8E · 3-[(2~{S},3~{R})-7-ethoxy-2-(3-ethoxy-4-methoxy-phenyl)-3-(hydroxymethyl)-2,3-dihydro-1-benzofuran-5-yl]propan-1-ol · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 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 | 435 | 0.72 | 0.82 | 47 | MG, W8E |
| 2 | 463 | 0.72 | 0.81 | 41 | MG, W8E |
| 3 | 211 | 0.58 | 0.80 | 25 | EDO |
| 4 | 166 | 0.56 | 0.81 | 21 | empty |
| 5 | 124 | 0.40 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 754 Ų buried · 10 hydrogen bonds · protein-protein
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 8WDN · PDBe 8WDN · UniProt Q08499
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