MolNFT v1 · #27606 · protein
Catalytic domain of human phosphodiesterase 4B in complex with vardenafil
1XOT · Camp-specific 3',5'-cyclic phosphodiesterase 4B: “Catalytic domain of human phosphodiesterase 4B in complex with vardenafil”. X-ray diffraction, 3 ligands (VDN, ZN, MG), 6 pockets (best druggability 0.69). MolNFT v1 #27606 on…
- PDB
- 1XOT
- 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
- VDN, ZN, MG
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Camp-specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.17) | protein | 323 | 67% helix, 0% strand | Q07343 |
Ligands and binding sites
- VDN · 2-{2-ethoxy-5-[(4-ethylpiperazin-1-yl)sulfonyl]phenyl}-5-methyl-7-propylimidazo[5,1-f][1,2,4]triazin-4(1H)-one · ligand · 2 copies · chains B, A
- ZN · Zinc ion · metal · 2 copies · chains B, A
- MG · Magnesium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.69 | 0.81 | 38 | MG, VDN |
| 2 | 423 | 0.69 | 0.81 | 47 | MG, VDN |
| 3 | 385 | 0.62 | 0.77 | 53 | empty |
| 4 | 232 | 0.61 | 0.81 | 22 | empty |
| 5 | 66 | 0.38 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- B–A · 839 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 1XOT · Catalytic Domain Of Human Phosphodiesterase 4B In Complex With Vardenafil · the same entry in another collection · chain B against B, 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 B 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 1XOT · PDBe 1XOT · UniProt Q07343
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