Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43373.34 
• Atom Count: 2971 
• Residue Count: 371 
• Unique protein chains: 2

4IE9

Bovine PKA C-alpha in complex with 3-pyridylmethyl-5-methyl-1H-pyrazole-3-carboxylate

• DOI: 10.2210/pdb4IE9/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens, Bos taurus
• Expression System: Escherichia coli


• Deposited: 2012-12-13 Released: 2013-05-01 
• Deposition Author(s): Dreyer, M.K., Schiffer, A., Lodge, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.232 
• R-Value Work: 0.177 

Literature

Accounting for Conformational Variability in Protein-Ligand Docking with NMR-Guided Rescoring

Skjaerven, L., Codutti, L., Angelini, A., Grimaldi, M., Latek, D., Monecke, P., Dreyer, M.K., Carlomagno, T.

(2013) J.Am.Chem.Soc. 135: 5819-5827

• PubMed: 23565800 
• DOI: 10.1021/ja4007468
• Primary Citation of Related Structures:  
  4IJ9


• PubMed Abstract: 
  

A key component to success in structure-based drug design is reliable information on protein-ligand interactions. Recent development in NMR techniques has accelerated this process by overcoming some of the limitations of X-ray crystallography and computational protein-ligand docking. In this work we present a new scoring protocol based on NMR-derived interligand INPHARMA NOEs to guide the selection of computationally generated docking modes. We demonstrate the performance in a range of scenarios, encompassing traditionally difficult cases such as docking to homology models and ligand dependent domain rearrangements. Ambiguities associated with sparse experimental information are lifted by searching a consensus solution based on simultaneously fitting multiple ligand pairs. This study provides a previously unexplored integration between molecular modeling and experimental data, in which interligand NOEs represent the key element in the rescoring algorithm. The presented protocol should be widely applicable for protein-ligand docking also in a different context from drug design and highlights the important role of NMR-based approaches to describe intermolecular ligand-receptor interactions.

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Organizational Affiliation: 

EMBL, Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
cAMP-dependent protein kinase catalytic subunit alpha	A	351	Bos taurus	Mutation(s): 0  Gene Names: PRKACA EC: 2.7.11.11
Find proteins for P00517 (Bos taurus) Go to Gene View: PRKACA Go to UniProtKB:  P00517

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
cAMP-dependent protein kinase inhibitor alpha	I	20	Homo sapiens	Mutation(s): 0  Gene Names: PKIA (PRKACN1)
Find proteins for P61925 (Homo sapiens) Go to Gene View: PKIA Go to UniProtKB:  P61925

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PZX	A	pyridin-3-ylmethyl 5-methyl-1H-pyrazole-3-carboxylate C11 H11 N3 O2 VPQUTEUTVVBFOS-UHFFFAOYSA-N
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.232 
• R-Value Work: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 73.060	α = 90.00
b = 75.320	β = 90.00
c = 79.880	γ = 90.00

Software Package:

Software Name	Purpose
MAR345	data collection
AMoRE	phasing
BUSTER	refinement
SCALA	data scaling
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-12-13 
• Released Date: 2013-05-01 
• Deposition Author(s): Dreyer, M.K., Schiffer, A., Lodge, J.

Revision History 

• Version 1.0: 2013-05-01
  Type: Initial release
• Version 1.1: 2017-11-15
  Type: Refinement description