Research workbench
Crystal structure of the catalytic domain of PDE4D2 complexed with compound 10D
Analyse Crystal structure of the catalytic domain of PDE4D2 complexed with compound 10D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SL5
- Type
- protein
- Length
- 1,302 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
- J25, 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 | 328 | 67% helix, 1% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 325 | 67% 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 | 66% helix, 1% strand | Q08499 |
Ligands and binding sites
- J25 · diethyl 2-[(thiophen-2-ylacetyl)amino]-4,7-dihydrothieno[2,3-c]pyridine-3,6(5H)-dicarboxylate · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · chains A
- 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 | 421 | 0.81 | 0.89 | 63 | EDO |
| 2 | 652 | 0.79 | 0.84 | 59 | EDO |
| 3 | 263 | 0.77 | 0.90 | 48 | empty |
| 4 | 235 | 0.76 | 0.90 | 43 | empty |
| 5 | 448 | 0.73 | 0.82 | 42 | ZN, J25 |
Interfaces
6 interfaces between chains.
- A–C · 959 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 938 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 688 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 679 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 238 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3SL5 · Crystal structure of the catalytic domain of PDE4D2 complexed with compound 10d · 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 3SL5 · PDBe 3SL5 · UniProt Q08499
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