MolNFT v1 · #70892 · protein
Catalytic domain of human phosphodiesterase 4B in complex with a coumarin-based inhibitor
3LY2 · Camp-specific 3',5'-cyclic phosphodiesterase 4B: “Catalytic domain of human phosphodiesterase 4B in complex with a coumarin-based inhibitor”. X-ray diffraction, 4 ligands (Z72, ZN, MG), 20 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 3LY2
- Type
- protein
- Length
- 2,672 residues
- Chains
- 8
- 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
- Z72, ZN, MG, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 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 | 345 | 63% helix, 1% strand | Q07343 |
| C, G, H | Camp-specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.17) | protein | 332 | 65% helix, 1% strand | Q07343 |
| D | Camp-specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.17) | protein | 328 | 66% helix, 1% strand | Q07343 |
| E | Camp-specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.17) | protein | 329 | 66% helix, 1% strand | Q07343 |
| F | Camp-specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.17) | protein | 329 | 66% helix, 1% strand | Q07343 |
Ligands and binding sites
- Z72 · 8-(cyclopentyloxy)-4-[(3,5-dichloropyridin-4-yl)amino]-7-methoxy-2H-chromen-2-one · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 925 | 0.86 | 0.87 | 115 | empty |
| 2 | 682 | 0.82 | 0.87 | 79 | SO4 |
| 3 | 910 | 0.81 | 0.83 | 89 | empty |
| 4 | 1098 | 0.81 | 0.82 | 98 | empty |
| 5 | 560 | 0.80 | 0.86 | 73 | empty |
Interfaces
14 interfaces between chains.
- B–G · 1172 Ų buried · 18 hydrogen bonds · protein-protein
- A–H · 1159 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1011 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1004 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 624 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3LY2 · Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor · the same entry in another collection · chain H against H, 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 E 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 Q07343
- Elsewhere: RCSB PDB 3LY2 · PDBe 3LY2 · UniProt Q07343
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