MolNFT v1 · #69248 · protein
Crystal structure of human PDE4B with 5-[3-[(1S,2S,4R)- BICYCLO[2.2.1]HEPT-2-yloxy]-4-methoxyp HENYL]TETRAHYDRO-2(1H)- pyrimidinone reveals ordering of the C-terminal helix residues 502- 509.
3KKT · Camp-specific 3',5'-cyclic phosphodiesterase 4B: “Crystal structure of human PDE4B with 5-[3-[(1S,2S,4R)- BICYCLO[2.2.1]HEPT-2-yloxy]-4-methoxyp…”. X-ray diffraction, 3 ligands (0CP, ZN, MG), 5 pockets (best druggability 0.82).…
- PDB
- 3KKT
- Type
- protein
- Length
- 685 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-specific 3',5'-cyclic phosphodiesterase 4B
- EC
- 3.1.4.17
- UniProt
- Q07343
- Ligands
- 0CP, ZN, MG
- Pockets
- 5 · best druggability 0.82
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 3.1.4.17) | protein | 347 | 65% helix, 1% strand | Q07343 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.17) | protein | 338 | 67% helix, 1% strand | Q07343 |
Ligands and binding sites
- 0CP · 5-{3-[(1S,2S,4R)-bicyclo[2.2.1]hept-2-yloxy]-4-methoxyphenyl}tetrahydropyrimidin-2(1H)-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
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.82 | 0.86 | 69 | 0CP, MG |
| 2 | 1097 | 0.81 | 0.82 | 101 | 0CP, MG |
| 3 | 61 | 0.33 | 0.76 | 15 | empty |
| 4 | 54 | 0.29 | 0.75 | 17 | empty |
| 5 | 54 | 0.28 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 873 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3KKT · Crystal structure of human PDE4b with 5-[3-[(1S,2S,4R)-Bicyclo[2.2.1]hept-2-yloxy]-4-metho… · the same entry in another collection · chain A against A, TM-score 1.00
- Q07343 · AlphaFold monomer V2.0 prediction for camp-specific 3',5'-cyclic phosphodiesterase 4B… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 3KKT · PDBe 3KKT · UniProt Q07343
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