Research workbench
Crystal structure of PDE8A catalytic domain in complex with clofarabine
Analyse Crystal structure of PDE8A catalytic domain in complex with clofarabine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CWA
- 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
- CFB, ZN, MG
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 72% 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 | 72% helix, 0% strand | O60658 |
Ligands and binding sites
- CFB · 2-chloro-9-(2-deoxy-2-fluoro-B -D-arabinofuranosyl)-9H-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
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.72 | 0.83 | 42 | MG, CFB |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7CWA · Crystal structure of PDE8A catalytic domain in complex with clofarabine · 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 7CWA · PDBe 7CWA · UniProt O60658
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.