MolNFT v1 · #28058 · protein
Catalytic domain of human phosphodiesterase 4D in complex with 3,5- dimethyl-1H-pyrazole-4-carboxylic acid ethyl ester
1Y2B · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Catalytic domain of human phosphodiesterase 4D in complex with 3,5- dimethyl-1H-pyrazole-4-carboxylic acid…”. X-ray diffraction, 3 ligands (DEE, ZN, MG), 5 pockets (best druggability…
- PDB
- 1Y2B
- 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
- DEE, ZN, MG
- Pockets
- 5 · best druggability 0.73
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 | 326 | 68% helix, 1% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 322 | 68% helix, 0% strand | Q08499 |
Ligands and binding sites
- DEE · 3,5-dimethyl-1H-pyrazole-4-carboxylic acid ethyl ester · 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 · 19 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 | 423 | 0.73 | 0.83 | 41 | MG, DEE, EDO |
| 2 | 459 | 0.71 | 0.81 | 39 | MG, DEE, EDO |
| 3 | 239 | 0.59 | 0.79 | 25 | EDO |
| 4 | 206 | 0.57 | 0.80 | 27 | EDO |
| 5 | 88 | 0.36 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 827 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1Y2B · Catalytic Domain Of Human Phosphodiesterase 4D In Complex 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 1Y2B · PDBe 1Y2B · UniProt Q08499
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