Research workbench
Crystal structure of of PDE2-inhibitor complex
Analyse Crystal structure of of PDE2-inhibitor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JIB
- Type
- protein
- Length
- 1,338 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-dependent 3',5'-cyclic phosphodiesterase
- EC
- 3.1.4.17
- UniProt
- O00408
- Ligands
- 1L6, ZN, MG
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 340 | 69% helix, 0% strand | O00408 |
| B | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 336 | 69% helix, 0% strand | O00408 |
| C | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 327 | 70% helix, 0% strand | O00408 |
| D | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 335 | 69% helix, 0% strand | O00408 |
Ligands and binding sites
- 1L6 · 1-(2-hydroxyethyl)-3-(2-methylbutan-2-yl)-5-[4-(2-methyl-1H-imidazol-1-yl)phenyl]-6,7-dihydropyrazolo[4,3-e][1,4]diazepin-8(1H)-one · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
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 | 985 | 0.84 | 0.85 | 75 | MG, 1L6 |
| 2 | 439 | 0.76 | 0.84 | 42 | MG, 1L6 |
| 3 | 449 | 0.74 | 0.83 | 42 | MG, 1L6 |
| 4 | 402 | 0.74 | 0.84 | 42 | MG, 1L6 |
| 5 | 828 | 0.74 | 0.78 | 68 | empty |
Interfaces
5 interfaces between chains.
- C–D · 887 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 764 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 760 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 447 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 87 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4JIB · Crystal structure of of PDE2-inhibitor complex · 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 O00408
- Elsewhere: RCSB PDB 4JIB · PDBe 4JIB · UniProt O00408
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