MolNFT v1 · #144879 · protein
Crystal structure of human phosphodiesterase 2A with 1-(2-chloro-5- isobutoxy-phenyl)-N,4-dimethyl-[1,2,4]TRIAZOLO[4,3-A]QUINOXALINE-8- carboxamide
6C7F · Cgmp-dependent 3',5'-cyclic phosphodiesterase: “Crystal structure of human phosphodiesterase 2A with 1-(2-chloro-5…”. X-ray diffraction, 3 ligands (EOS, ZN, MG), 8 pockets (best druggability 0.77). MolNFT v1 #144879 on GenesisL1: 3D…
- PDB
- 6C7F
- Type
- protein
- Length
- 994 residues
- Chains
- 3
- 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
- EOS, ZN, MG
- Pockets
- 8 · best druggability 0.77
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 | 339 | 71% helix, 0% strand | O00408 |
| B | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 336 | 70% helix, 0% strand | O00408 |
| C | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 319 | 68% helix, 0% strand | O00408 |
Ligands and binding sites
- EOS · 1-[2-chloro-5-(2-methylpropoxy)phenyl]-N,4-dimethyl[1, 2,4]triazolo[4,3-a]quinoxaline-8-carboxamide · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.77 | 0.86 | 41 | EOS, MG |
| 2 | 462 | 0.76 | 0.85 | 42 | EOS, MG |
| 3 | 441 | 0.76 | 0.85 | 41 | EOS, MG |
| 4 | 742 | 0.75 | 0.80 | 79 | empty |
| 5 | 105 | 0.64 | 0.89 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 843 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 202 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 52 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6C7F · 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 6C7F · PDBe 6C7F · UniProt O00408
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