Research workbench
Crystal structure of the catalytic domain of PDE4D2 with compound 12C
Analyse Crystal structure of the catalytic domain of PDE4D2 with compound 12C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SL6
- Type
- protein
- Length
- 1,301 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-specific 3',5'-cyclic phosphodiesterase 4D
- EC
- 3.1.4.17
- UniProt
- Q08499
- Ligands
- JN8, ZN
- Pockets
- 13 · best druggability 0.81
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 3.1.4.17) | protein | 327 | 67% helix, 1% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 325 | 66% helix, 1% strand | Q08499 |
| C | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 325 | 68% helix, 1% strand | Q08499 |
| D | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 324 | 68% helix, 1% strand | Q08499 |
Ligands and binding sites
- JN8 · cyclopentyl 6-(ethylcarbamoyl)-2-[(thiophen-2-ylacetyl)amino]-4,5,6,7-tetrahydrothieno[2,3-c]pyridine-3-carboxylate · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 30 copies · chains A, C, B, D
- DMS · Dimethyl sulfoxide · additive · chains B
- 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
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.81 | 0.90 | 65 | EDO |
| 2 | 341 | 0.79 | 0.89 | 53 | EDO |
| 3 | 164 | 0.73 | 0.91 | 21 | EDO |
| 4 | 208 | 0.73 | 0.88 | 41 | EDO |
| 5 | 471 | 0.72 | 0.82 | 45 | ZN, JN8 |
Interfaces
6 interfaces between chains.
- A–C · 908 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 905 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 699 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 688 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 226 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3SL6 · Crystal structure of the catalytic domain of PDE4D2 with compound 12c · 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 3SL6 · PDBe 3SL6 · UniProt Q08499
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