4YXS image
Entry Detail
PDB ID:
4YXS
Title:
CAMP-DEPENDENT PROTEIN KINASE PKA CATALYTIC SUBUNIT WITH PKI-5-24
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2015-03-23
Release Date:
2015-05-20
Method Details:
Experimental Method:
Resolution:
2.11 Å
R-Value Free:
0.23
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:cAMP-dependent protein kinase catalytic subunit alpha
Chain IDs:A
Chain Length:350
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Description:cAMP-dependent protein kinase inhibitor alpha
Chain IDs:B (auth: I)
Chain Length:20
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
SEP A SER modified residue
TPO A THR modified residue
Ligand Molecules
Primary Citation
A combination of spin diffusion methods for the determination of protein-ligand complex structural ensembles.
Angew.Chem.Int.Ed.Engl. 54 6511 6515 (2015)
PMID: 25877959 DOI: 10.1002/anie.201500671

Abstact

Structure-based drug design (SBDD) is a powerful and widely used approach to optimize affinity of drug candidates. With the recently introduced INPHARMA method, the binding mode of small molecules to their protein target can be characterized even if no spectroscopic information about the protein is known. Here, we show that the combination of the spin-diffusion-based NMR methods INPHARMA, trNOE, and STD results in an accurate scoring function for docking modes and therefore determination of protein-ligand complex structures. Applications are shown on the model system protein kinase A and the drug targets glycogen phosphorylase and soluble epoxide hydrolase (sEH). Multiplexing of several ligands improves the reliability of the scoring function further. The new score allows in the case of sEH detecting two binding modes of the ligand in its binding site, which was corroborated by X-ray analysis.

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Primary Citation of related structures