MolNFT v1 · #148514 · protein
Crystal structure of the PDE4D catalytic domain in complex with gebr- 26G
6F8X · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Crystal structure of the PDE4D catalytic domain in complex with gebr- 26G”. X-ray diffraction, 3 ligands (D08, MG, ZN), 5 pockets (best druggability 0.73). MolNFT v1 #148514 on…
- PDB
- 6F8X
- Type
- protein
- Length
- 646 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
- D08, 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 | 322 | 68% helix, 1% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 324 | 66% helix, 0% strand | Q08499 |
Ligands and binding sites
- D08 · 2-[(5~{R})-3-(3-cyclopentyloxy-4-methoxy-phenyl)-4,5-dihydro-1,2-oxazol-5-yl]-~{N},~{N}-bis(2-hydroxyethyl)ethanamide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.73 | 0.83 | 42 | MG, D08, EDO |
| 2 | 451 | 0.71 | 0.81 | 39 | MG, D08 |
| 3 | 214 | 0.57 | 0.80 | 21 | empty |
| 4 | 201 | 0.56 | 0.79 | 24 | empty |
| 5 | 67 | 0.31 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 762 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6F8X · Crystal structure of the PDE4D catalytic domain in complex with GEBR-26g · 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 6F8X · PDBe 6F8X · UniProt Q08499
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