Research workbench
Crystal structure of human phosphodiesterase 2A with N-(1-adamantyl)- 1-(2-chloro-5-isobutoxy-phenyl)-4-methyl-[1,2,4]TRIAZOLO[4,3- A]QUINOXALINE-8-carboxamide
Analyse Crystal structure of human phosphodiesterase 2A with N-(1-adamantyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C7G
- Type
- protein
- Length
- 1,340 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
- EOY, ZN, MG
- Pockets
- 12 · best druggability 0.84
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 | 338 | 69% helix, 0% strand | O00408 |
| C | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 326 | 68% helix, 0% strand | O00408 |
| D | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 335 | 69% helix, 0% strand | O00408 |
Ligands and binding sites
- EOY · 1-[2-chloro-5-(2-methylpropoxy)phenyl]-4-methyl-N-[(3S, 5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-yl][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
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.84 | 0.85 | 106 | EOY, MG |
| 2 | 470 | 0.77 | 0.85 | 42 | EOY, MG |
| 3 | 449 | 0.76 | 0.85 | 44 | EOY, MG |
| 4 | 429 | 0.76 | 0.85 | 43 | EOY, MG |
| 5 | 1008 | 0.74 | 0.77 | 90 | empty |
Interfaces
5 interfaces between chains.
- C–D · 892 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 819 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 806 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 505 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 124 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6C7G · 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 6C7G · PDBe 6C7G · UniProt O00408
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