Research workbench
Crystal structure of AKT1 in complex with covalent-allosteric AKT inhibitor 24B
Analyse Crystal structure of AKT1 in complex with covalent-allosteric AKT inhibitor 24B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HHJ
- Type
- protein
- Length
- 410 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rac-alpha SERINE/THREONINE-protein kinase
- EC
- 2.7.11.1
- UniProt
- P31749
- Ligands
- G4H
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rac-alpha SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 410 | 31% helix, 24% strand | P31749 |
Ligands and binding sites
- G4H · ~{N}-[1-methyl-2-oxidanylidene-3-[1-[[4-(5-oxidanylidene-3-phenyl-6~{H}-1,6-naphthyridin-2-yl) phenyl]methyl]piperidin-4-yl]benzimidazol-5-yl]propanamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.80 | 0.82 | 81 | G4H |
| 2 | 209 | 0.56 | 0.79 | 37 | empty |
| 3 | 107 | 0.46 | 0.79 | 15 | empty |
| 4 | 163 | 0.46 | 0.76 | 25 | empty |
| 5 | 65 | 0.35 | 0.76 | 14 | empty |
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 6HHJ · Crystal Structure of AKT1 in Complex with Covalent-Allosteric AKT Inhibitor 24b · the same entry in another collection · chain A against A, TM-score 1.00
- P31749 · AlphaFold monomer V2.0 prediction for rac-alpha SERINE/THREONINE- protein kinase (P31749) · a predicted model of the same protein · chain A against A, TM-score 0.67
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 P31749
- Elsewhere: RCSB PDB 6HHJ · PDBe 6HHJ · UniProt P31749
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