Research workbench
Crystal Structure of AKT1 in Complex with Covalent-Allosteric AKT Inhibitor 16a
Analyse Crystal Structure of AKT1 in Complex with Covalent-Allosteric AKT Inhibitor 16a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S9W
- Type
- protein
- Length
- 411 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Homo sapiens
- Molecule
- RAC-alpha serine/threonine-protein kinase
- EC
- 2.7.11.1
- UniProt
- P31749
- Ligands
- L1Z
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.3 · 1 distinct chain · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAC-alpha serine/threonine-protein kinase (EC 2.7.11.1) | protein | 411 | 33% helix, 24% strand | P31749 |
Ligands and binding sites
- L1Z · ~{N}-[3-[1-[[4-(5-methyl-6-oxidanylidene-3-phenyl-1~{H}-pyrazin-2-yl)phenyl]methyl]piperidin-4-yl]-2-oxidanylidene-1~{H}-benzimidazol-5-yl]propanamide · ligand · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.81 | 0.82 | 101 | L1Z |
| 2 | 438 | 0.67 | 0.79 | 47 | empty |
| 3 | 112 | 0.51 | 0.81 | 20 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6S9W · Crystal structure of AKT1 in complex with covalent-allosteric AKT inhibitor 16A · 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 0.68
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 6S9W · PDBe 6S9W · UniProt P31749
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