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Crystal structure of human phosphodiesterase 2A with 1-(2- chlorophenyl)-N,4-dimethyl-[1,2,4]TRIAZOLO[4,3-A]QUINOXALINE-8- carboxamide
Analyse Crystal structure of human phosphodiesterase 2A 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
- 6C7E
- Type
- protein
- Length
- 1,339 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
- EOG, ZN, MG
- Pockets
- 14 · 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 | 342 | 70% helix, 0% strand | O00408 |
| B | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 339 | 69% helix, 0% strand | O00408 |
| C | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 331 | 68% 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
- EOG · 1-(2-chlorophenyl)-N,4-dimethyl[1,2,4]triazolo[4,3-a]quinoxaline-8-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
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.85 | 0.85 | 107 | EOG, MG |
| 2 | 405 | 0.74 | 0.84 | 40 | EOG, MG |
| 3 | 385 | 0.73 | 0.84 | 40 | EOG, MG |
| 4 | 866 | 0.73 | 0.78 | 79 | empty |
| 5 | 377 | 0.73 | 0.84 | 41 | EOG, MG |
Interfaces
5 interfaces between chains.
- C–D · 885 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 832 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 814 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 455 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 108 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6C7E · Crystal structure of human phosphodiesterase 2A 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 6C7E · PDBe 6C7E · UniProt O00408
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