MolNFT v1 · #113340 · protein
Human PDK1 kinase domain in complex with allosteric compound 7 bound to the pif-pocket
5ACK · 3-phosphoinositide-dependent protein kinase 1: “Human PDK1 kinase domain in complex with allosteric compound 7 bound to the pif-pocket”. X-ray diffraction, 3 ligands (ATP, SVQ, NA), 2 pockets (best druggability 0.61). MolNFT v1…
- PDB
- 5ACK
- Type
- protein
- Length
- 287 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
- ATP, SVQ, NA
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1) | protein | 287 | 41% helix, 18% strand | O15530 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- SVQ · 1-(4-chlorophenethyl)-2-(2-chlorophenyl)-6-oxopiperidine-3-carboxylic acid · ligand · chains A
- NA · Sodium ion · metal · 3 copies · chains A
- DTD · Dithiane diol · additive · chains A
- DMS · Dimethyl sulfoxide · 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 | 288 | 0.61 | 0.79 | 32 | ATP, NA |
| 2 | 66 | 0.38 | 0.79 | 24 | empty |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 5ACK · Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the PIF-Pocket · 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 5ACK · PDBe 5ACK · UniProt O15530
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