Research workbench
Bromine sad partially resolves multiple binding modes for PKA inhibitor H-89
Analyse Bromine sad partially resolves multiple binding modes for PKA inhibitor H-89 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VQH
- Type
- protein
- Length
- 367 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
- P17612, P61925
- Ligands
- IQB
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 37% 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 | 347 | 37% helix, 16% strand | P17612 |
| B | Camp-dependent protein kinase inhibitor alpha | protein | 20 | 30% helix, 5% strand | P61925 |
Ligands and binding sites
- IQB · N-[2-(4-bromocinnamylamino)ethyl]-5-isoquinoline sulfonamide · ligand · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.81 | 0.91 | 41 | IQB |
| 2 | 116 | 0.54 | 0.82 | 13 | empty |
| 3 | 213 | 0.49 | 0.75 | 26 | empty |
| 4 | 86 | 0.41 | 0.79 | 20 | empty |
| 5 | 72 | 0.33 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1046 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 3VQH · Bromine SAD partially resolves multiple binding modes for PKA inhibitor H-89 · the same entry in another collection · chain A against A, TM-score 1.00
- P17612 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase catalytic subunit… · a predicted model of the same protein · chain A 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 P17612
- Every structure of UniProt P61925
- Elsewhere: RCSB PDB 3VQH · PDBe 3VQH · UniProt P17612 · UniProt P61925
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