MolNFT v1 · #138369 · protein
Crystal structure of PDE4D2 in complex with inhibitor (S_ZL-N-91)
5WH6 · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Crystal structure of PDE4D2 in complex with inhibitor (S_ZL-N-91)”. X-ray diffraction, 3 ligands (AKJ, MG, ZN), 6 pockets (best druggability 0.73). MolNFT v1 #138369 on GenesisL1: 3D…
- PDB
- 5WH6
- Type
- protein
- Length
- 651 residues
- Chains
- 2
- 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
- AKJ, MG, ZN
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 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 | 326 | 67% helix, 1% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 325 | 67% helix, 1% strand | Q08499 |
Ligands and binding sites
- AKJ · 1-[4-(difluoromethoxy)-3-{[(3S)-oxolan-3-yl]oxy}phenyl]-3-methylbutan-1-one · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.73 | 0.83 | 44 | AKJ, MG |
| 2 | 472 | 0.72 | 0.82 | 41 | AKJ, MG |
| 3 | 228 | 0.59 | 0.80 | 25 | empty |
| 4 | 177 | 0.58 | 0.81 | 20 | empty |
| 5 | 120 | 0.39 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 818 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5WH6 · Crystal structure of PDE4D2 in complex with inhibitor (S_Zl-n-91) · 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 5WH6 · PDBe 5WH6 · UniProt Q08499
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