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Human phosphodiesterase 4B catalytic domain in complex with a pyrrolidinyl inhibitor.
Analyse Human phosphodiesterase 4B catalytic domain in complex with a pyrrolidinyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OHJ
- Type
- protein
- Length
- 671 residues
- Chains
- 2
- 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
- 9VE, ZN, MG
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 66% 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 | 336 | 65% helix, 1% strand | Q07343 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.53) | protein | 335 | 66% helix, 1% strand | Q07343 |
Ligands and binding sites
- 9VE · [(1~{S})-2-[3,5-bis(chloranyl)-1-oxidanyl-pyridin-1-ium-4-yl]-1-[4-[bis(fluoranyl)methoxy]-3-(cyclopropylmethoxy)phenyl]ethyl] (2~{S})-1-[3-(dimethylcarbamoyl)phenyl]sulfonylpyrrolidine-2-carboxylate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.73 | 0.81 | 40 | MG, 9VE |
| 2 | 455 | 0.72 | 0.82 | 43 | MG, 9VE |
| 3 | 301 | 0.62 | 0.79 | 36 | empty |
| 4 | 206 | 0.52 | 0.77 | 30 | empty |
| 5 | 176 | 0.51 | 0.78 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 718 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5OHJ · Human phosphodiesterase 4B catalytic domain in complex with a pyrrolidinyl 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 5OHJ · PDBe 5OHJ · UniProt Q07343
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