Research workbench
Crystal structure of PDE8A catalytic domain in complex with 2C
Analyse Crystal structure of PDE8A catalytic domain in complex with 2C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CWF
- Type
- protein
- Length
- 338 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- High affinity camp-specific and ibmx-insensitive 3',5'- cyclic phosphodiesterase 8A
- EC
- 3.1.4.53
- UniProt
- O60658
- Ligands
- GJR, ZN, MG
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | High affinity camp-specific and ibmx-insensitive 3',5'- cyclic phosphodiesterase 8A (EC 3.1.4.53) | protein | 338 | 71% helix, 0% strand | O60658 |
Ligands and binding sites
- GJR · 9-[[4-[2,2-bis(fluoranyl)ethoxy]pyridin-2-yl]methyl]-2-chloranyl-purin-6-amine · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.76 | 0.85 | 43 | MG, GJR |
| 2 | 59 | 0.31 | 0.76 | 12 | empty |
| 3 | 68 | 0.30 | 0.73 | 17 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7CWF · Crystal structure of PDE8A catalytic domain in complex with 2c · the same entry in another collection · chain A against A, TM-score 1.00
- O60658 · AlphaFold monomer V2.0 prediction for high affinity camp-specific and ibmx-insensitive… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O60658
- Elsewhere: RCSB PDB 7CWF · PDBe 7CWF · UniProt O60658
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