Research workbench
Catalytic domain of human phosphodiesterase 4B in complex with piclamilast
Analyse Catalytic domain of human phosphodiesterase 4B in complex with piclamilast in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XM4
- Type
- protein
- Length
- 646 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-specific 3',5'-cyclic phosphodiesterase 4B
- EC
- 3.1.4.17
- UniProt
- Q07343
- Ligands
- PIL, ZN, MG
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Camp-specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.17) | protein | 323 | 66% helix, 1% strand | Q07343 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.72 | 0.83 | 38 | MG, PIL |
| 2 | 422 | 0.71 | 0.82 | 40 | MG, PIL |
| 3 | 506 | 0.66 | 0.77 | 63 | empty |
| 4 | 64 | 0.33 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 865 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (artifact).
Compared structures
- 1XM4 · Catalytic Domain Of Human Phosphodiesterase 4B In Complex With Piclamilast · the same entry in another collection · chain A against A, TM-score 1.00
- Q07343 · AlphaFold monomer V2.0 prediction for camp-specific 3',5'-cyclic phosphodiesterase 4B… · 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 Q07343
- Elsewhere: RCSB PDB 1XM4 · PDBe 1XM4 · UniProt Q07343
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