Research workbench
Crystal structure of human PDE1B catalytic domain in complex with inhibitor 16J (6-(4-methoxybenzyl)-9-((tetrahydro-2H-pyran-4-yl) methyl)-8,9,10,11-TETRAHYDROPYRIDO[4',3':4,5]THIENO[3,2-E][1,2, 4]TRIAZOLO[1,5-C]PYRIMIDIN-5(6H)-one)
Analyse Crystal structure of human PDE1B catalytic domain in complex with inhibitor 16J… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UOY
- Type
- protein
- Length
- 321 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CALCIUM/CALMODULIN-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B
- EC
- 3.1.4.17
- UniProt
- Q01064
- Ligands
- 8HM, ZN, MG
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CALCIUM/CALMODULIN-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B (EC 3.1.4.17) | protein | 321 | 71% helix, 0% strand | Q01064 |
Ligands and binding sites
- 8HM · 6-[(4-methoxyphenyl)methyl]-9-[(oxan-4-yl)methyl]-8,9, 10,11-tetrahydropyrido[4',3':4,5]thieno[3,2-E][1,2, 4]triazolo[1,5-c]pyrimidin-5(6H)-one · ligand · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.73 | 0.83 | 41 | MG, 8HM |
| 2 | 56 | 0.41 | 0.81 | 17 | empty |
Compared structures
- 5UOY · Crystal structure of human PDE1B catalytic domain in complex with inhibitor 16j… · the same entry in another collection · chain A against A, TM-score 1.00
- Q01064 · AlphaFold monomer V2.0 prediction for CALCIUM/CALMODULIN-dependent 3',5'-cyclic… · a predicted model of the same protein · 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 Q01064
- Elsewhere: RCSB PDB 5UOY · PDBe 5UOY · UniProt Q01064
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