MolNFT v1 · #134952 · protein
Crystal structure of human phosphodiesterase 4D in complex with a tetrafluoranline compound
5TKB · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Crystal structure of human phosphodiesterase 4D in complex with a tetrafluoranline compound”. X-ray diffraction, 4 ligands (7DJ, ZN, MG), 12 pockets (best druggability 0.88). MolNFT…
- PDB
- 5TKB
- Type
- protein
- Length
- 1,297 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-specific 3',5'-cyclic phosphodiesterase 4D
- EC
- 3.1.4.53
- UniProt
- Q08499
- Ligands
- 7DJ, ZN, MG, SO4
- Pockets
- 12 · best druggability 0.88
Structure
x-ray diffraction · 4 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 | 326 | 67% helix, 1% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 323 | 66% helix, 0% strand | Q08499 |
| C | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 323 | 67% helix, 0% strand | Q08499 |
| D | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 325 | 66% helix, 1% strand | Q08499 |
Ligands and binding sites
- 7DJ · N-[(2R)-2,3-dihydroxy-2-methylpropyl]-8-(methylamino)-6-[(2,3,5,6-tetrafluorophenyl)amino]imidazo[1,2-b]pyridazine-3-carboxamide · 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
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- EOH · Ethanol · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1094 | 0.88 | 0.89 | 146 | EOH |
| 2 | 634 | 0.79 | 0.84 | 53 | EOH |
| 3 | 437 | 0.72 | 0.82 | 41 | MG, 7DJ |
| 4 | 442 | 0.72 | 0.82 | 46 | MG, 7DJ |
| 5 | 420 | 0.71 | 0.82 | 39 | MG, 7DJ |
Interfaces
6 interfaces between chains.
- B–D · 904 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 899 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 878 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 854 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 247 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5TKB · Crystal structure of human phosphodiesterase 4D in complex with a tetrafluoranline… · 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 5TKB · PDBe 5TKB · UniProt Q08499
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