Research workbench
Crystal structure of human phosphodiesterase 2A in complex with 3,3- difluoro-1-[(4-fluoro-3-IODOPHENYL)CARBONYL]-5-{5-methyl-[1,2, 4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL}PIPERIDINE
Analyse Crystal structure of human phosphodiesterase 2A in complex with 3,3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U00
- Type
- protein
- Length
- 1,355 residues
- Chains
- 4
- 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
- 7OV, ZN, MG
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 341 | 69% helix, 0% strand | O00408 |
| B, C | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 339 | 69% helix, 0% strand | O00408 |
| D | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 336 | 70% helix, 0% strand | O00408 |
Ligands and binding sites
- 7OV · [(5S)-3,3-difluoro-5-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)piperidin-1-yl](4-fluoro-3-iodophenyl)methanone · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 946 | 0.82 | 0.84 | 74 | 7OV, MG |
| 2 | 425 | 0.74 | 0.84 | 41 | 7OV, MG |
| 3 | 396 | 0.73 | 0.84 | 38 | 7OV, MG |
| 4 | 582 | 0.72 | 0.80 | 74 | empty |
| 5 | 380 | 0.72 | 0.83 | 38 | 7OV, MG |
Interfaces
5 interfaces between chains.
- A–B · 845 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 822 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 804 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 472 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 168 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5U00 · CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A IN COMPLEX WITH… · 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 5U00 · PDBe 5U00 · UniProt O00408
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