Research workbench
PDE2 complexed with 2-[6-fluoro-8-methylsulfonyl-9-[(1R)-1-[4- (TRIFLUOROMETHYL)PHENYL]ETHYL]-1,2,3,4-tetrahydrocarbazol-1-YL]ACETIC acid
Analyse PDE2 complexed with 2-[6-fluoro-8-methylsulfonyl-9-[(1R)-1-[4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BLF
- Type
- protein
- Length
- 697 residues
- Chains
- 2
- 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
- DY1, ZN, MG
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 348 | 67% helix, 0% strand | O00408 |
| B | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 349 | 68% helix, 0% strand | O00408 |
Ligands and binding sites
- DY1 · [(1S)-6-fluoro-8-(methylsulfonyl)-9-{(1R)-1-[4-(trifluoromethyl)phenyl]ethyl}-2,3,4,9-tetrahydro-1H-carbazol-1-yl]acetic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.76 | 0.85 | 42 | DY1, MG |
| 2 | 483 | 0.76 | 0.84 | 41 | DY1, MG |
| 3 | 440 | 0.72 | 0.82 | 60 | empty |
| 4 | 403 | 0.67 | 0.80 | 53 | empty |
| 5 | 55 | 0.29 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 942 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6BLF · PDE2 complexed with 2-[6-fluoro-8-methylsulfonyl-9-[(1R)-1-[4-(trifluoromethyl)phenyl]ethy… · 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 6BLF · PDBe 6BLF · UniProt O00408
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