MolNFT v1 · #124034 · protein
PDE4D crystal structure in complex with small molecule inhibitor
5K32 · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “PDE4D crystal structure in complex with small molecule inhibitor”. X-ray diffraction, 3 ligands (6Q2, ZN, MG), 6 pockets (best druggability 0.69). MolNFT v1 #124034 on GenesisL1: 3D…
- PDB
- 5K32
- Type
- protein
- Length
- 643 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
- 6Q2, ZN, MG
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 68% 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, 0% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 321 | 68% helix, 1% strand | Q08499 |
Ligands and binding sites
- 6Q2 · 4-[(3-methoxyphenyl)amino]-2-phenyl-7,8-dihydro-1,6-naphthyridin-5(6H)-one · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 32 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.69 | 0.81 | 40 | MG, 6Q2, EDO |
| 2 | 423 | 0.67 | 0.79 | 44 | MG, 6Q2, EDO |
| 3 | 207 | 0.60 | 0.81 | 21 | EDO |
| 4 | 247 | 0.60 | 0.79 | 26 | EDO |
| 5 | 87 | 0.36 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 796 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5K32 · PDE4D crystal structure in complex with small molecule inhibitor · 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 5K32 · PDBe 5K32 · UniProt Q08499
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