Research workbench
Crystal structure of human phosphodiesterase 2A in complex with [1,2, 4]TRIAZOLO[1,5-A]PYRIMIDIN-7-yl}-N-(naphthalene-2-YL)PIPERIDINE-3- carboxamide
Analyse Crystal structure of human phosphodiesterase 2A in complex with [1,2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TZ3
- Type
- protein
- Length
- 1,342 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
- 7OM, ZN, MG
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 4 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 | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 340 | 69% helix, 0% strand | O00408 |
| C | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 334 | 69% helix, 0% strand | O00408 |
| D | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 327 | 69% helix, 0% strand | O00408 |
Ligands and binding sites
- 7OM · (3~{R})-1-(5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)-~{N}-naphthalen-2-yl-piperidine-3-carboxamide · 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
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.85 | 0.86 | 108 | 7OM, MG |
| 2 | 713 | 0.75 | 0.80 | 90 | empty |
| 3 | 380 | 0.74 | 0.84 | 39 | 7OM, MG |
| 4 | 424 | 0.74 | 0.83 | 42 | 7OM, MG |
| 5 | 392 | 0.73 | 0.83 | 37 | 7OM, MG |
Interfaces
5 interfaces between chains.
- C–D · 846 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 833 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 744 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 460 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 116 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5TZ3 · 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 5TZ3 · PDBe 5TZ3 · UniProt O00408
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