MolNFT v1 · #135720 · protein
PDE2 catalytic domain complexed with inhibitors
5U7D · Cgmp-dependent 3',5'-cyclic phosphodiesterase: “PDE2 catalytic domain complexed with inhibitors”. X-ray diffraction, 3 ligands (19F, ZN, MG), 9 pockets (best druggability 0.77). MolNFT v1 #135720 on GenesisL1: 3D structure, binding…
- PDB
- 5U7D
- Type
- protein
- Length
- 1,004 residues
- Chains
- 3
- 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
- 19F, ZN, MG
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 338 | 70% helix, 0% strand | O00408 |
| B | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 328 | 68% helix, 0% strand | O00408 |
Ligands and binding sites
- 19F · 2-(3,4-dimethoxybenzyl)-7-[(2R,3R)-2-hydroxy-6-phenylhexan-3-yl]-5-methylimidazo[5,1-f][1,2,4]triazin-4(3H)-one · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.77 | 0.86 | 40 | 19F, MG |
| 2 | 438 | 0.76 | 0.85 | 38 | 19F, MG |
| 3 | 1141 | 0.76 | 0.78 | 115 | empty |
| 4 | 482 | 0.74 | 0.83 | 42 | 19F, MG |
| 5 | 110 | 0.42 | 0.76 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 808 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 107 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 56 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5U7D · PDE2 catalytic domain complexed with inhibitors · 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 5U7D · PDBe 5U7D · UniProt O00408
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