MolNFT v1 · #148702 · protein
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-1086
6FEB · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-1086”. X-ray diffraction, 3 ligands (D5Z, MG, ZN), 5 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 6FEB
- Type
- protein
- Length
- 648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-specific 3',5'-cyclic phosphodiesterase 4D
- EC
- 3.1.4.53
- UniProt
- Q08499
- Ligands
- D5Z, MG, ZN
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 325 | 67% helix, 0% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 323 | 68% helix, 1% strand | Q08499 |
Ligands and binding sites
- D5Z · (4aS,8aR)-2-[1-(2-aminoquinazolin-4-yl)piperidin-4-yl]-4-(3,4-dimethoxyphenyl)-1,2,4a,5,8,8a-hexahydrophthalazin-1-one · ligand · 3 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.73 | 0.83 | 44 | EDO, D5Z, MG |
| 2 | 426 | 0.72 | 0.82 | 40 | EDO, D5Z, MG |
| 3 | 709 | 0.70 | 0.77 | 81 | EDO |
| 4 | 56 | 0.31 | 0.76 | 13 | empty |
| 5 | 53 | 0.27 | 0.74 | 17 | EDO |
Interfaces
1 interface between chains.
- A–B · 827 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6FEB · Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1086 · 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 6FEB · PDBe 6FEB · UniProt Q08499
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