Research workbench
CYCLIC GMP-AMP SYNTHASE in complex with compound 16 inhibitor: 7-hydroxy-N-methyl-5-phenylpyrazolo[1,5-a]pyrimidine-3-carboxamide
Analyse CYCLIC GMP-AMP SYNTHASE in complex with compound 16 inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NFG
- Type
- protein
- Length
- 694 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.76
- Source
- Homo sapiens
- Molecule
- Cyclic gmp-AMP synthase
- EC
- 2.7.7.86
- UniProt
- Q8N884
- Ligands
- KKP, ZN
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.76 · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclic gmp-AMP synthase (EC 2.7.7.86) | protein | 348 | 46% helix, 18% strand | Q8N884 |
| B | Cyclic gmp-AMP synthase (EC 2.7.7.86) | protein | 346 | 45% helix, 18% strand | Q8N884 |
Ligands and binding sites
- KKP · 7-hydroxy-N-methyl-5-phenylpyrazolo[1,5-a]pyrimidine-3-carboxamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.74 | 0.79 | 77 | KKP |
| 2 | 656 | 0.72 | 0.79 | 62 | KKP |
| 3 | 244 | 0.57 | 0.78 | 24 | empty |
| 4 | 133 | 0.43 | 0.75 | 25 | empty |
| 5 | 67 | 0.35 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 710 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6NFG · Cyclic gmp-AMP synthase in complex with compound 16 inhibitor: 7… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8N884 · AlphaFold monomer V2.0 prediction for cyclic gmp-AMP synthase (Q8N884) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q8N884
- Elsewhere: RCSB PDB 6NFG · PDBe 6NFG · UniProt Q8N884
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