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Crystal structure of the phosphoinositide-dependent kinase- 1 (pdk-1)CATALYTIC domain bound to a dibenzonaphthyridine inhibitor
Analyse Crystal structure of the phosphoinositide-dependent kinase- 1 (pdk-1)CATALYTIC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R7B
- Type
- protein
- Length
- 274 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoinositide-dependent protein kinase 1
- EC
- 2.7.11.1
- UniProt
- O15530
- Ligands
- PSE, 253, SO4
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1) | protein | 274 | 40% helix, 18% strand | O15530 |
Ligands and binding sites
- PSE · O-phosphoethanolamine · ligand · chains A
- 253 · 10,11-dimethoxy-4-methyldibenzo[c,f]-2,7-naphthyridine-3,6-diamine · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.63 | 0.79 | 35 | SO4, 253 |
| 2 | 72 | 0.29 | 0.72 | 16 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2R7B · Crystal Structure of the Phosphoinositide-dependent Kinase-1 (PDK-1)Catalytic Domain… · the same entry in another collection · chain A against A, TM-score 1.00
- O15530 · AlphaFold monomer V2.0 prediction for 3-phosphoinositide-dependent protein kinase 1… · 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 O15530
- Elsewhere: RCSB PDB 2R7B · PDBe 2R7B · UniProt O15530
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