Research workbench
Crystal structure of the catalytic domain of PDE4D2 with (S)-N-(3-{1- [1-(3-cyclopropylmethoxy-4-difluoromethoxyphenyl)-2-(1-oxypyridin-4- yl)-ethyl]-1H-pyrazl-3-YL}PHENYL)ACETAMIDE
Analyse Crystal structure of the catalytic domain of PDE4D2 with (S)-N-(3-{1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V9B
- Type
- protein
- Length
- 1,309 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-specific 3',5'-cyclic phosphodiesterase 4D
- EC
- 3.1.4.17
- UniProt
- Q08499
- Ligands
- IHM, ZN
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 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 | 331 | 67% helix, 1% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 327 | 68% helix, 1% strand | Q08499 |
| C | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 325 | 66% helix, 1% strand | Q08499 |
| D | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 326 | 66% helix, 1% strand | Q08499 |
Ligands and binding sites
- IHM · N-(3-{1-[(1S)-1-[3-(cyclopropylmethoxy)-4-(difluoromethoxy)phenyl]-2-(1-oxidopyridin-4-yl)ethyl]-1H-pyrazol-3-yl}phenyl)acetamide · 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
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.81 | 0.91 | 46 | empty |
| 2 | 234 | 0.77 | 0.91 | 40 | empty |
| 3 | 165 | 0.74 | 0.91 | 21 | empty |
| 4 | 194 | 0.73 | 0.90 | 41 | empty |
| 5 | 192 | 0.72 | 0.89 | 31 | empty |
Interfaces
6 interfaces between chains.
- A–C · 921 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 908 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 695 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 629 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 240 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3V9B · Crystal structure of the catalytic domain of PDE4D2 with… · 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 3V9B · PDBe 3V9B · UniProt Q08499
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