MolNFT v1 · #145790 · protein
PDE2 in complex with compound 7
6CYD · Cgmp-dependent 3',5'-cyclic phosphodiesterase: “PDE2 in complex with compound 7”. X-ray diffraction, 3 ligands (FKG, ZN, MG), 6 pockets (best druggability 0.75). MolNFT v1 #145790 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6CYD
- Type
- protein
- Length
- 691 residues
- Chains
- 2
- 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
- FKG, ZN, MG
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 343 | 67% helix, 0% strand | O00408 |
| B | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 348 | 67% helix, 0% strand | O00408 |
Ligands and binding sites
- FKG · 3-(hydroxymethyl)-6-methyl-1-{(1S)-1-[4-(trifluoromethyl)phenyl]ethyl}-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-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
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.75 | 0.85 | 40 | MG, FKG, EDO |
| 2 | 440 | 0.75 | 0.84 | 42 | MG, FKG, EDO |
| 3 | 367 | 0.67 | 0.81 | 48 | empty |
| 4 | 357 | 0.66 | 0.80 | 46 | empty |
| 5 | 85 | 0.53 | 0.85 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 998 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6CYD · PDE2 in complex with compound 7 · 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 6CYD · PDBe 6CYD · UniProt O00408
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