4IJ9

Bovine PKA C-alpha in complex with 2-[[5-(4-pyridyl)-1H-1,2,4-triazol-3-yl]sulfanyl]-1-(2-thiophenyl)ethanone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1021/ja4007468
  • Primary Citation of Related Structures:  

  • 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 com ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase catalytic subunit alpha
A
350Bos taurusMutation(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
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase inhibitor alpha
I
20Homo sapiensMutation(s): 0 
Gene Names: PKIA (PRKACN1)
Find proteins for P61925 (Homo sapiens)
Go to Gene View: PKIA
Go to UniProtKB:  P61925
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PTV
Query on PTV

Download SDF File 
Download CCD File 
A
2-[[5-(4-pyridyl)-1H-1,2,4-triazol-3-yl]sulfanyl]-1-(2-thiophenyl)ethanone
C13 H10 N4 O S2
PCHCUBVZNSWLHT-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.680α = 90.00
b = 75.610β = 90.00
c = 79.050γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
MAR345data collection
CCP4model building
CCP4phasing
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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