Research workbench
Discovery of 2-pyrimidyl-5-amidothiophenes as novel and potent inhibitors for AKT: synthesis and sar studies
Analyse Discovery of 2-pyrimidyl-5-amidothiophenes as novel and potent inhibitors for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GU8
- Type
- protein
- Length
- 357 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase, alpha-catalytic subunit; Inhibitor of camp-dependent…
- EC
- 2.7.1.37
- UniProt
- P17612
- Ligands
- 796
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-dependent protein kinase, alpha-catalytic subunit (EC 2.7.1.37) | protein | 337 | 37% helix, 16% strand | P17612 |
| C | Inhibitor of camp-dependent protein kinase | protein | 20 | 35% helix, 10% strand | — |
Ligands and binding sites
- 796 · N-[(1S)-2-amino-1-(2,4-dichlorobenzyl)ethyl]-5-[2-(methylamino)pyrimidin-4-yl]thiophene-2-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.80 | 0.89 | 43 | 796 |
| 2 | 102 | 0.43 | 0.78 | 20 | empty |
| 3 | 67 | 0.39 | 0.78 | 13 | empty |
| 4 | 53 | 0.28 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–C · 1016 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 2GU8 · Discovery of 2-Pyrimidyl-5-Amidothiophenes as Novel and Potent Inhibitors for AKT… · 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 0.99
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
- Elsewhere: RCSB PDB 2GU8 · PDBe 2GU8 · UniProt P17612
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