Research workbench
Crystal structure of PDE4D catalytic domain complexed with compound 18D
Analyse Crystal structure of PDE4D catalytic domain complexed with compound 18D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F2M
- Type
- protein
- Length
- 648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 3 of camp-specific 3',5'-cyclic phosphodiesterase 4D
- EC
- 3.1.4.53
- UniProt
- Q08499
- Ligands
- 1GF, ZN, MG
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 3 of camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 325 | 69% helix, 1% strand | Q08499 |
| B | Isoform 3 of camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 323 | 66% helix, 1% strand | Q08499 |
Ligands and binding sites
- 1GF · (~{Z})-4-[9-[(4-fluorophenyl)methoxy]-8-methoxy-2,2-dimethyl-7-(3-methylbut-2-enyl)-6-oxidanylidene-pyrano[3,2-b]xanthen-5-yl]oxybut-2-enoic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 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 | 439 | 0.72 | 0.82 | 47 | MG, 1GF |
| 2 | 433 | 0.70 | 0.81 | 46 | MG, 1GF |
| 3 | 204 | 0.60 | 0.81 | 22 | empty |
| 4 | 201 | 0.54 | 0.78 | 24 | empty |
| 5 | 112 | 0.38 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 778 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7F2M · Crystal structure of PDE4D catalytic domain complexed with compound 18d · 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 7F2M · PDBe 7F2M · UniProt Q08499
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