Research workbench
Crystal structure of human phosphodiesterase 4D with bound allosteric modulator
Analyse Crystal structure of human phosphodiesterase 4D with bound allosteric modulator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IAD
- Type
- protein
- Length
- 1,356 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-specific 3',5'-cyclic phosphodiesterase 4D
- EC
- 3.1.4.17
- UniProt
- Q08499
- Ligands
- 15X, ZN, MG
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 340 | 68% helix, 1% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 338 | 67% helix, 1% strand | Q08499 |
| C | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 339 | 67% helix, 1% strand | Q08499 |
| D | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 339 | 67% helix, 1% strand | Q08499 |
Ligands and binding sites
- 15X · 1-{4-[(2-fluoro-6-methoxy-3'-nitrobiphenyl-3-yl)methyl]phenyl}urea · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.85 | 0.86 | 119 | 15X, MG |
| 2 | 457 | 0.83 | 0.90 | 51 | 15X, MG |
| 3 | 450 | 0.82 | 0.90 | 61 | 15X, MG |
| 4 | 454 | 0.82 | 0.89 | 57 | 15X, MG |
| 5 | 448 | 0.82 | 0.89 | 71 | empty |
Interfaces
6 interfaces between chains.
- B–D · 926 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 897 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 707 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 695 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 237 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3IAD · Crystal structure of human phosphodiesterase 4D with bound allosteric modulator · 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 Q08499
- Elsewhere: RCSB PDB 3IAD · PDBe 3IAD · UniProt Q08499
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.