Research workbench
Catalytic domain of human phosphodiesterase 4B2B in complex with a quinoline inhibitor
Analyse Catalytic domain of human phosphodiesterase 4B2B in complex with a quinoline… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GWT
- Type
- protein
- Length
- 336 residues
- Chains
- 1
- 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
- 066, ARS, ZN, MG
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.17) | protein | 336 | 66% helix, 1% strand | Q07343 |
Ligands and binding sites
- 066 · 6-{[3-(dimethylcarbamoyl)phenyl]sulfonyl}-4-[(3-methoxyphenyl)amino]-8-methylquinoline-3-carboxamide · ligand · chains A
- ARS · Arsenic · metal · 4 copies · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.71 | 0.81 | 49 | 066, MG, ARS, GOL |
| 2 | 73 | 0.42 | 0.80 | 18 | ARS |
| 3 | 62 | 0.33 | 0.76 | 21 | empty |
| 4 | 54 | 0.27 | 0.75 | 13 | empty |
Compared structures
- 3GWT · Catalytic domain of human phosphodiesterase 4B2B in complex with a quinoline inhibitor · 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 0.98
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 3GWT · PDBe 3GWT · UniProt Q07343
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