MolNFT v1 · #143763 · protein
Crystal structure of PDE2 in complex with compound 16
6B96 · Cgmp-dependent 3',5'-cyclic phosphodiesterase: “Crystal structure of PDE2 in complex with compound 16”. X-ray diffraction, 3 ligands (CZV, ZN, MG), 4 pockets (best druggability 0.81). MolNFT v1 #143763 on GenesisL1: 3D structure…
- PDB
- 6B96
- Type
- protein
- Length
- 690 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
- CZV, ZN, MG
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 66% 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 | 347 | 66% helix, 0% strand | O00408 |
Ligands and binding sites
- CZV · 6-chloro-N-{1-[4-(trifluoromethyl)phenyl]cyclopropyl}-1H-pyrazolo[3,4-d]pyrimidin-4-amine · 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 · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.81 | 0.82 | 92 | EDO |
| 2 | 438 | 0.75 | 0.84 | 40 | MG, CZV, EDO |
| 3 | 427 | 0.75 | 0.84 | 42 | MG, CZV |
| 4 | 72 | 0.31 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 804 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6B96 · Crystal Structure of PDE2 in complex with compound 16 · 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 6B96 · PDBe 6B96 · UniProt O00408
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