Research workbench
Crystal structure of PDE4A10 in complex with inhibitor npv
Analyse Crystal structure of PDE4A10 in complex with inhibitor npv in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QYK
- Type
- protein
- Length
- 669 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic AMP-specific phosphodiesterase HSPDE4A10
- UniProt
- Q9H3H2
- Ligands
- NPV, ZN, MG
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclic AMP-specific phosphodiesterase HSPDE4A10 | protein | 334 | 65% helix, 1% strand | Q9H3H2 |
| B | Cyclic AMP-specific phosphodiesterase HSPDE4A10 | protein | 335 | 65% helix, 1% strand | Q9H3H2 |
Ligands and binding sites
- NPV · 4-[8-(3-nitrophenyl)-1,7-naphthyridin-6-yl]benzoic 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 594 | 0.83 | 0.88 | 65 | NPV, MG |
| 2 | 330 | 0.77 | 0.88 | 38 | NPV, MG |
| 3 | 63 | 0.34 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 632 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2QYK · Crystal structure of PDE4A10 in complex with inhibitor NPV · 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 Q9H3H2
- Elsewhere: RCSB PDB 2QYK · PDBe 2QYK · UniProt Q9H3H2
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