MolNFT v1 · #170942 · protein
Crystal structure of the camp-dependent protein kinase a in complex with 1,7-naphthyridin-8-amine (soaked) and pki (5-24)
6YNR · Camp-dependent protein kinase catalytic subunit alpha: “Crystal structure of the camp-dependent protein kinase a in complex with 1,7-naphthyridin-8-amine (soaked)…”. X-ray diffraction, 1 ligand (O72), 3 pockets (best druggability…
- PDB
- 6YNR
- Type
- protein
- Length
- 360 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase catalytic subunit alpha; Camp-dependent protein kinase…
- EC
- 2.7.11.11
- UniProt
- P25321, P63248
- Ligands
- O72
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 341 | 38% helix, 16% strand | P25321 |
| B | Camp-dependent protein kinase inhibitor alpha | protein | 19 | 37% helix, 5% strand | P63248 |
Ligands and binding sites
- O72 · 1,7-naphthyridin-8-amine · ligand · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.78 | 0.88 | 43 | O72 |
| 2 | 99 | 0.52 | 0.82 | 14 | empty |
| 3 | 89 | 0.36 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 888 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 6YNR · Crystal structure of the cAMP-dependent protein kinase A in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P63248 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase inhibitor alpha… · a predicted model of the same protein · chain B against A, TM-score 0.42
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 P25321
- Every structure of UniProt P63248
- Elsewhere: RCSB PDB 6YNR · PDBe 6YNR · UniProt P25321 · UniProt P63248
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