Research workbench
Crystal structure of PDE9A(Q453E) in complex with inhibitor BAY73-6691
Analyse Crystal structure of PDE9A(Q453E) in complex with inhibitor BAY73-6691 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QI3
- Type
- protein
- Length
- 650 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- High affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9A
- EC
- 3.1.4.35
- UniProt
- O76083
- Ligands
- PDB, ZN, MG
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | High affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9A (EC 3.1.4.35) | protein | 325 | 70% helix, 0% strand | O76083 |
Ligands and binding sites
- PDB · 1-(2-chlorophenyl)-6-[(2R)-3,3,3-trifluoro-2-methylpropyl]-1,7-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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.74 | 0.84 | 40 | PDB, MG |
| 2 | 371 | 0.73 | 0.84 | 42 | PDB, MG |
| 3 | 76 | 0.41 | 0.79 | 19 | empty |
| 4 | 92 | 0.37 | 0.75 | 18 | empty |
| 5 | 50 | 0.35 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 866 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3QI3 · Crystal structure of PDE9A(Q453E) in complex with inhibitor BAY73-6691 · the same entry in another collection · chain A against A, TM-score 1.00
- O76083 · AlphaFold monomer V2.0 prediction for high affinity cgmp-specific 3',5'-cyclic… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O76083
- Elsewhere: RCSB PDB 3QI3 · PDBe 3QI3 · UniProt O76083
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