MolNFT v1 · #124143 · protein
Human phospodiesterase 4B in complex with pyridyloxy-benzoxaborole based inhibitor
5K6J · Camp-specific 3',5'-cyclic phosphodiesterase 4B: “Human phospodiesterase 4B in complex with pyridyloxy-benzoxaborole based inhibitor”. X-ray diffraction, 3 ligands (6QQ, ZN, MG), 2 pockets (best druggability 0.74). MolNFT v1 #124143…
- PDB
- 5K6J
- Type
- protein
- Length
- 323 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-specific 3',5'-cyclic phosphodiesterase 4B
- EC
- 3.1.4.53
- UniProt
- Q07343
- Ligands
- 6QQ, ZN, MG
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 67% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.53) | protein | 323 | 67% helix, 1% strand | Q07343 |
Ligands and binding sites
- 6QQ · 6-[[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1(6),2,4-trien-3-yl]oxy]-5-chloranyl-2-(4-oxidanylidenepentoxy)pyridine-3-carbonitrile · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 17 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.74 | 0.83 | 40 | MG, 6QQ, EDO |
| 2 | 52 | 0.27 | 0.75 | 14 | empty |
Compared structures
- 5K6J · Human Phospodiesterase 4B in complex with pyridyloxy-benzoxaborole based 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 Q07343
- Elsewhere: RCSB PDB 5K6J · PDBe 5K6J · UniProt Q07343
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.