MolNFT v1 · #66320 · protein
Catalytic domain of human phosphodiesterase 4B2B in complex with a tetrahydrobenzothiophene inhibitor
3HMV · Camp-specific 3',5'-cyclic phosphodiesterase 4B: “Catalytic domain of human phosphodiesterase 4B2B in complex with a tetrahydrobenzothiophene inhibitor”. X-ray diffraction, 3 ligands (HBT, ZN, MG), 6 pockets (best druggability…
- PDB
- 3HMV
- Type
- protein
- Length
- 702 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
- HBT, ZN, MG
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 65% 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 | 351 | 65% helix, 1% strand | Q07343 |
Ligands and binding sites
- HBT · (6S)-6-methyl-2-{[(2-nitrophenyl)carbonyl]amino}-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.84 | 0.91 | 44 | MG, HBT |
| 2 | 1042 | 0.82 | 0.83 | 93 | MG, HBT |
| 3 | 123 | 0.37 | 0.73 | 24 | empty |
| 4 | 53 | 0.35 | 0.78 | 15 | empty |
| 5 | 83 | 0.31 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 653 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3HMV · Catalytic domain of human phosphodiesterase 4B2B in complex with a… · 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 0.94
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 3HMV · PDBe 3HMV · UniProt Q07343
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