MolNFT v1 · #27600 · protein
Catalytic domain of human phosphodiesterase 4D in complex with piclamilast
1XON · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Catalytic domain of human phosphodiesterase 4D in complex with piclamilast”. X-ray diffraction, 3 ligands (PIL, ZN, MG), 5 pockets (best druggability 0.72). MolNFT v1 #27600 on…
- PDB
- 1XON
- Type
- protein
- Length
- 648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-specific 3',5'-cyclic phosphodiesterase 4D
- EC
- 3.1.4.17
- UniProt
- Q08499
- Ligands
- PIL, ZN, MG
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 322 | 68% helix, 0% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 326 | 67% helix, 1% strand | Q08499 |
Ligands and binding sites
- PIL · 3-(cyclopentyloxy)-N-(3,5-dichloropyridin-4-yl)-4-methoxybenzamide · 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 · 35 copies · chains A, B
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
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 | 430 | 0.72 | 0.82 | 39 | MG, PIL, EDO |
| 2 | 493 | 0.71 | 0.80 | 46 | MG, PIL, EDO |
| 3 | 225 | 0.59 | 0.80 | 26 | EDO |
| 4 | 196 | 0.58 | 0.80 | 26 | EDO |
| 5 | 121 | 0.38 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 801 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1XON · Catalytic Domain Of Human Phosphodiesterase 4D In Complex With Piclamilast · 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 1XON · PDBe 1XON · UniProt Q08499
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