MolNFT v1 · #118389 · protein
Crystal structure of PVX_084705 with bound 1-tert-butyl-3-(3- chlorophenoxy)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-amine inhibitor
5F0A · Cgmp-dependent protein kinase, putative: “Crystal structure of PVX_084705 with bound 1-tert-butyl-3-(3…”. X-ray diffraction, 1 ligand (1FB), 11 pockets (best druggability 0.75). MolNFT v1 #118389 on GenesisL1: 3D structure, binding…
- PDB
- 5F0A
- Type
- protein
- Length
- 811 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-dependent protein kinase, putative
- UniProt
- A5K0N4
- Ligands
- 1FB
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-dependent protein kinase, putative | protein | 811 | 35% helix, 27% strand | A5K0N4 |
Ligands and binding sites
- 1FB · 1-tert-butyl-3-(3-chlorophenoxy)-1H-pyrazolo[3,4-d]pyrimidin-4-amine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.75 | 0.79 | 67 | empty |
| 2 | 286 | 0.73 | 0.86 | 31 | 1FB |
| 3 | 122 | 0.60 | 0.85 | 19 | empty |
| 4 | 220 | 0.47 | 0.74 | 21 | empty |
| 5 | 131 | 0.46 | 0.78 | 18 | empty |
Compared structures
- 5F0A · CRYSTAL STRUCTURE OF PVX_084705 WITH BOUND 1-tert-butyl-3-(3-chlorophenoxy)-1H-pyrazolo[3… · the same entry in another collection · chain A against A, TM-score 1.00
- A5K0N4 · AlphaFold monomer V2.0 prediction for cgmp-dependent protein kinase (A5K0N4) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 A5K0N4
- Elsewhere: RCSB PDB 5F0A · PDBe 5F0A · UniProt A5K0N4
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