MolNFT v1 · #126195 · protein
Human PDK1 kinase domain in complex with compound PS653 bound to the ATP-binding site
5LVL · 3-phosphoinositide-dependent protein kinase 1: “Human PDK1 kinase domain in complex with compound PS653 bound to the ATP-binding site”. X-ray diffraction, 1 ligand (537), 2 pockets (best druggability 0.63). MolNFT v1 #126195 on…
- PDB
- 5LVL
- Type
- protein
- Length
- 286 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-phosphoinositide-dependent protein kinase 1
- EC
- 2.7.11.1
- UniProt
- O15530
- Ligands
- 537
- 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 | 3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1) | protein | 286 | 40% helix, 18% strand | O15530 |
Ligands and binding sites
- 537 · 2,6-dihydroanthra/1,9-cd/pyrazol-6-one · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A
- DTD · Dithiane diol · additive · 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 | 328 | 0.63 | 0.79 | 36 | 537 |
| 2 | 84 | 0.37 | 0.76 | 24 | empty |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 5LVL · Human PDK1 Kinase Domain in Complex with Compound PS653 Bound to the ATP-Binding Site · the same entry in another collection · chain A against A, TM-score 1.00
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 5LVL · PDBe 5LVL · UniProt O15530
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