MolNFT v1 · #102253 · protein
Crystal structure of the catalytic domain of PDE4D2 with compound 2
4OGB · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Crystal structure of the catalytic domain of PDE4D2 with compound 2”. X-ray diffraction, 2 ligands (2SR, ZN), 14 pockets (best druggability 0.79). MolNFT v1 #102253 on GenesisL1: 3D…
- PDB
- 4OGB
- Type
- protein
- Length
- 1,298 residues
- Chains
- 4
- 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
- 2SR, ZN
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 328 | 66% helix, 0% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 321 | 66% helix, 1% strand | Q08499 |
| C | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 325 | 68% helix, 1% strand | Q08499 |
| D | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 324 | 67% helix, 1% strand | Q08499 |
Ligands and binding sites
- 2SR · (2R)-8-(3,4-dimethoxyphenyl)-6-methyl-2-(tetrahydro-2H-pyran-4-yl)-2H-chromen-4-ol · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 32 copies · chains A, C, D, B
- DMS · Dimethyl sulfoxide · additive · 6 copies · chains A, B, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.79 | 0.89 | 58 | EDO |
| 2 | 780 | 0.79 | 0.82 | 66 | EDO, PEG |
| 3 | 436 | 0.72 | 0.82 | 40 | 2SR, ZN |
| 4 | 444 | 0.71 | 0.81 | 43 | 2SR, ZN, EDO, DMS |
| 5 | 416 | 0.70 | 0.82 | 38 | 2SR, ZN |
Interfaces
6 interfaces between chains.
- A–C · 917 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 884 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 710 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 670 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 235 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4OGB · Crystal structure of the catalytic domain of PDE4D2 with compound 2 · 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 4OGB · PDBe 4OGB · UniProt Q08499
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