Research workbench
PDE4D complexed with inhibitor
Analyse PDE4D complexed with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4W1O
- Type
- protein
- Length
- 1,285 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-specific 3',5'-cyclic phosphodiesterase 4D
- EC
- 3.1.4.53
- UniProt
- Q08499
- Ligands
- 3GJ, ZN
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 322 | 67% helix, 1% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 325 | 67% helix, 0% strand | Q08499 |
| C | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 321 | 69% helix, 0% strand | Q08499 |
| D | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 317 | 68% helix, 0% strand | Q08499 |
Ligands and binding sites
- 3GJ · N-(3,5-dichloropyridin-4-yl)-3-[(3-ethyl-1,2-oxazol-5-yl)methoxy]-4-methoxybenzamide · 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
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.73 | 0.83 | 41 | 3GJ, ZN |
| 2 | 492 | 0.72 | 0.81 | 40 | 3GJ, ZN |
| 3 | 449 | 0.72 | 0.82 | 39 | 3GJ, ZN |
| 4 | 892 | 0.71 | 0.76 | 76 | empty |
| 5 | 438 | 0.71 | 0.81 | 41 | 3GJ, ZN |
Interfaces
5 interfaces between chains.
- A–B · 474 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 409 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 282 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 265 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 230 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4W1O · PDE4D complexed with inhibitor · the same entry in another collection · chain B against B, 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 4W1O · PDBe 4W1O · UniProt Q08499
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